1. PHOTOSYNTHESIS

2. Overview:
A. Step One: Transferring radiant energy to chemical energy e-
Energy of photon
Transferred to an electron e-

3. A. Step Two: storing that chemical energy in the bonds of molecules
Overview:
A. Step Two: storing that chemical energy in the bonds of molecules e-
C6 (glucose)
ATP
ADP+P
6 CO2 e-

4. Light Dependent Reaction Light Independent Reaction
Overview:
A. Step Two: storing that chemical energy in the bonds of molecules e-
C6 (glucose)
ATP
ADP+P
6 CO2 e-
Light Dependent Reaction
Light Independent Reaction

5. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation e-
Used by photoheterotrophs:
Purple non-sulphur bacteria, green non-sulphur bacteria, and heliobacteria
PS I
“photosystems” are complexes of chlorophyll molecules containing Mg, nested in the inner membrane of bacteria and chloroplasts.

6. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
e- acceptor e-
PS I
“photosystems” are complexes of chlorophyll molecules containing Mg, nested in the inner membrane of bacteria and chloroplasts.

7. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
e- acceptor e- e-
The electron is transferred to an electron transport chain
PS I
The electron transport chain is nested in the inner membrane, as well; like in mitochondria….

8. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
e- acceptor e-
ATP e-
ADP+P
The electron is passed down the chain, H+ are pumped out, they flood back in and ATP is made.
PS I
The electron transport chain is nested in the inner membrane, as well; like in mitochondria… and chemiosmosis occurs.

9. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
e- acceptor e-
ATP e-
ADP+P
An electron is excited by sunlight, and the energy is used to make ATP. The electron is returned to the photosystem….CYCLIC PHOSPHORYLATION.
PS I
The electron transport chain is nested in the inner membrane, as well; like in mitochondria… and chemiosmosis occurs.

10. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
b. Sulpher bacteria
e- acceptor e-
Purple and green sulphur bacteria
ATP e-
ADP+P
PS I
An electron is excited by sunlight, and the energy is used to make ATP. The electron is returned to the photosystem….CYCLIC PHOSPHORYLATION…..
BUT something else can happen…

11. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
b. Sulpher bacteria
e- acceptor e-
NADP
NADPH
ATP e-
ADP+P
PS I
The electron can be passed to NADP, reducing NADP to NADP- (+H+)

12. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
b. Sulpher bacteria
e- acceptor e-
NADP
NADPH
ATP
IF this happens, the electron is NOT recycled back to PSI.
For the process to continue, an electron must be stripped from another molecule and transferred to the PS to be excited by sunlight… e-
ADP+P
PS I
The electron can be passed to NADP, reducing NADP to NADP- (+H+)

13. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
b. Sulpher bacteria
e- acceptor e-
NADP
NADPH
ATP
IF this happens, the electron is NOT recycled back to PSI.
For the process to continue, an electron must be stripped from another molecule and transferred to the PS to be exited by sunlight… e-
ADP+P
PS I
H2S
2e + 2H+ + S
The Photosystem is more electronegative than H2S, and can strip electrons from this molecule – releasing sulphur gas….

14. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
b. Sulpher bacteria
e- acceptor e-
PS I
ADP+P
ATP
NADP
NADPH
H2S
2e + 2H+ + S
So, through these reactions, both ATP and NADPH are produced; sulphur gas is released as a waste product. These organisms are limited to living in an environment with H2S!!! (Sulphur springs).

15. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
a. Cyclic phosphorylation
b. Sulpher bacteria
e- acceptor e-
NADP
NADPH
So, through these reactions, both ATP and NADPH are produced; sulphur gas is released as a waste product. These organisms are limited to living in an environment with H2S!!! (Sulphur springs).
ATP e-
ADP+P
PS I
If photosynthesis could evolve to strip electrons from a more abundant electron donor, life could expand from these limited habitats… hmmm…. H2S…. H2S….
H2S
2e + 2H+ + S

17. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
2. Advanced System
e- acceptor
Cyanobacteria, algae, plants
PS I
PS II
RIGHT! H2O!!! But water holds electrons more strongly than H2S; this process didn’t evolve until a PS evolved that could strip electrons from water… PSII.

18. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
2. Advanced System
e- acceptor e- e-
PS I
PS II
Photons excite electrons in both photosystems…

19. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
2. Advanced System
e- acceptor e- e-
ATP
ADP+P
PS I
PS II
The electron from PSII is passed down the ETC, making ATP, to PSI

21. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
2. Advanced System
e- acceptor
NADP
NADPH e-
ATP
ADP+P
PS I e-
PS II
The electron from PSI is passed to NADP to make NADPH

22. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
2. Advanced System
e- acceptor
NADP
NADPH e-
ATP
ADP+P
PS I e-
The e- from PSII has “filled the hole” vacated by the electron lost from PSI.
PS II

23. A. Step 1: The Light Dependent Reaction: 1. Primitive Systems
2. Advanced System
e- acceptor
NADP
NADPH e-
PS II
2H2O
4e + 4H O (O2)
ATP
ADP+P
PS I e-
Water is split to harvest electrons; oxygen gas is released as a waste product.

24. Light Dependent Reaction Light Independent Reaction
Those were the light dependent reactions; reactions in which photosynthetic organisms transform radiant energy into chemical bond energy in ATP (and NADPH). e-
C6 (glucose)
ATP
ADP+P
6 CO2 e-
Light Dependent Reaction
Light Independent Reaction

25. Light Dependent Reaction Light Independent Reaction
A. Step 1: The Light Dependent Reaction:
B: Step 2: The Light-Independent Reaction: e-
C6 (glucose)
ATP
ADP+P
6 CO2 e-
Light Dependent Reaction
Light Independent Reaction

26. CO2
B. The Light Independent Reaction C6 C5
RuBP
2 C3 (PGA)
A molecule of CO2 binds to Ribulose biphosphate, making a 6-carbon molecule. This molecule is unstable, and splits into 2 3-carbon molecules of phosphoglycerate (PGA)

27. 6CO2
B. The Light Independent Reaction
6C6
6C5
RuBP
12 C3 (PGA)
Now, it is easier to understand these reactions if we watch the simultaneous reactions involving 6 CO2 molecules

28. 6CO2 6C6 6C5 12 C3 10 C3 2 C3 B. The Light Independent Reaction C6
RuBP
12 C3
ATP
ADP+P
10 C3
2 C3 C6
(Glucose)
NADPH
NADP
2 of the 12 PGA are used to make glucose, using energy from ATP and the reduction potential of NADPH… essentially, the H is transferred to the PGA, making carbohydrate from carbon dioxide.

29. 6CO2 6C6 6C5 12 C3 10 C3 2 C3 B. The Light Independent Reaction C6
RuBP
6CO2
6C6
12 C3
2 C3 C6
(Glucose)
10 C3
ATP
ADP+P
NADPH
NADP
B. The Light Independent Reaction
More energy is used to rearrange the 10 C3 molecules (30 carbons) into 6 C5 molecules (30 carbons); regenerating the 6 RuBP.

30. Review

31. A History of Photosynthesis
Photosynthesis evolved early; at least 3.8 bya – bacterial mats like these stromatolites date to that age, and earlier microfossils exist that look like cyanobacteria. Also, CO2 levels drop (Calvin cycle + dissolved in rain)

32. A History of Photosynthesis
What kind of photosynthesis was this???

33. A History of Photosynthesis
What kind of photosynthesis was this???
Cyclic phosphorylation and Sulphur photosynthesis, because it was non-oxygenic.

34. A History of Photosynthesis
And 2.3 bya is when we see the oldest banded iron formations, demonstrating for the first time that iron crystals were exposed to atmospheric oxygen during sedimentation.

35. Carboniferous: mya
This is the period when our major deposits of fossil fuel were laid down as biomass that did NOT decompose. So, that carbon was NOT returned to the atmosphere as CO2…lots of photosynthesis and less decomposition means a decrease in CO2 and an increase in O2 in the atmosphere…

36. Cell Biology
I. Overview
II. Membranes: How Matter Get in and Out of Cells
III. Harvesting Energy: Respiration and Photosynthesis
IV. Protein Synthesis

37. IV. Protein Synthesis
Why is this important?
Well…what do proteins DO?

38. IV. Protein Synthesis
Why is this important?
Well…what do proteins DO?
Think about it this way:
sugars, fats, lipids, nucleic acids and proteins, themselves, are broken down and built up through chemical reactions catalyzed by enzymes.
So everything a cell IS, and everything it DOES, is either done by proteins or is done by molecules put together by proteins.

39. IV. Protein Synthesis
A. Overview
A T G C T G A C T A C T G
T A C G A CT G A T G A C
Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION
(t-RNA)
(r-RNA)
U G C U G A C U A C U
(m-RNA)

40. IV. Protein Synthesis
A. Overview
A T G C T G A C T A C T G
T A C G A CT G A T G A C
Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION
(t-RNA)
(r-RNA)
U G C U G A C U A C U
(m-RNA)
Eukaryotic RNA and some prokaryotic RNA have regions cut out… this is RNA SPLICING

41. R-RNA is complexed with proteins to form ribosomes.
IV. Protein Synthesis
A. Overview
A T G C T G A C T A C T G
T A C G A CT G A T G A C
R-RNA is complexed with proteins to form ribosomes.
Specific t-RNA’s bind to specific amino acids.
(t-RNA)
(r-RNA)
U G C U G A C U A C U
Amino acid
(m-RNA)
ribosome

42. IV. Protein Synthesis A. Overview A T G C T G A C T A C T G
T A C G A CT G A T G A C
The ribosome reads the m-RNA. Based on the sequence of nitrogenous bases in the m-RNA, a specific sequence of amino acids (carried to the ribosome by t-RNA’s) is linked together to form a protein. This is TRANSLATION.
(t-RNA)
(r-RNA)
U G C U G A C U A C U
Amino acid
(m-RNA)
ribosome

43. POST-TRANSLATIONAL MODIFICATION. (t-RNA) (r-RNA)
IV. Protein Synthesis
A. Overview
A T G C T G A C T A C T G
T A C G A CT G A T G A C
The protein product may be modified (have a sugar, lipid, nucleic acid, or another protein added) and/or spliced to become a functional protein. This is
POST-TRANSLATIONAL MODIFICATION.
(t-RNA)
(r-RNA)
U G C U G A C U A C U
Amino acid
(m-RNA)
ribosome
glycoprotein

44. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
a. The message is on one strand of the double helix - the sense strand: 3’ 5’
sense
A C T A T A C G T A C A A A C G G T T A T A C T A C T T T
T G A T A T G C A T G T T T G C C A A T A T G A T G A A A
nonsense 5’ 3’
“TAG A CAT” message makes ‘sense’
“ATC T GTA” ‘nonsense’ limited by complementation

45. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
a. The message is on one strand of the double helix - the sense strand: 3’ 5’
sense
A C T A T A C G T A C A A A C G G T T A T A C T A C T T T
T G A T A T G C A T G T T T G C C A A T A T G A T G A A A
nonsense 5’ 3’
exon
intron
exon
In all eukaryotic genes and in some prokaryotic sequences, there are introns and exons. There may be multiple introns of varying length in a gene. Genes may be several thousand base-pairs long. This is a simplified example!

46. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
b. The cell 'reads' the correct strand based on the location of the promoter, the anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase.
Promoter 3’ 5’
sense
A C T A T A C G T A C A A A C G G T T A T A C T A C T T T
T G A T A T G C A T G T T T G C C A A T A T G A T G A A A
nonsense 5’ 3’
exon
intron
exon
Promoters have sequences recognized by the RNA Polymerase. They bind in particular orientation.

47. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
b. The cell 'reads' the correct strand based on the location of the promoter, the anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase.
Promoter 3’ 5’
sense
A C T A T A C G T A C A A A C G G T T A T A C T A C T T T
G C A U GUUU G C C A A U AUG A U G A
T G A T A T G C A T G T T T G C C A A T A T G A T G A A A
nonsense 5’ 3’
exon
intron
exon
Strand separate
RNA Polymerase can only synthesize RNA in a 5’3’ direction, so they only read the anti-parallel, 3’5’ strand (‘sense’ strand).

48. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
c. Transcription ends at a sequence called the 'terminator'.
Promoter
Terminator 3’ 5’
sense
A C T A T A C G T A C A A A C G G T T A T A C T A C T T T
G C A U GUUU G C C A A U AUG A U G A
T G A T A T G C A T G T T T G C C A A T A T G A T G A A A
nonsense 5’ 3’
exon
intron
exon
Terminator sequences destabilize the RNA Polymerase and the enzyme decouples from the DNA, ending transcription

49. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
c. Transcription ends at a sequence called the 'terminator'.
Promoter
Terminator 3’ 5’
sense
A C T A T A C G T A C A A A C G G T T A T A C T A C T T T
G C A U GUUU G C C A A U AUG A U G A
T G A T A T G C A T G T T T G C C A A T A T G A T G A A A
nonsense 5’ 3’
exon
intron
exon
Initial RNA PRODUCT:

50. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
c. Transcription ends at a sequence called the 'terminator'.
Promoter
Terminator 3’ 5’
sense
A C T A T A C G T A C A A A C G G T T A T A C T A C T T T
T G A T A T G C A T G T T T G C C A A T A T G A T G A A A
nonsense 5’ 3’
intron
exon
G C A U GUUU G C C A A U AUG A U G A
Initial RNA PRODUCT:

51. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
intron
exon
Initial RNA PRODUCT:
G C A U GUUU G C C A A U
AUG A
U G A
Introns are spliced out, and exons are spliced together. Sometimes these reactions are catalyzed by the intron, itself, or other catalytic RNA molecules called “ribozymes”.

52. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
intron
exon
Final RNA PRODUCT:
AUG A
G C A U GUUU G C C A A U
U G A
This final RNA may be complexed with proteins to form a ribosome (if it is r-RNA), or it may bind amino acids (if it is t-RNA), or it may be read by a ribosome, if it is m-RNA and a recipe for a protein.

53. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
a. m-RNA attaches to the ribosome at the 5' end.
M-RNA:
G C A U G U U U G C C A A U
U G A

54. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
a. m-RNA attaches to the ribosome at the 5' end.
M-RNA:
G C A U G U U U G C C A A U
U G A
It then reads down the m-RNA, one base at a time, until an ‘AUG’ sequence (start codon) is positioned in the first reactive site.

55. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
a. m-RNA attaches to the ribosome at the 5' end.
b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex.
Meth
M-RNA:
G C A U G U U U G C C A A U
U G A

56. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
a. m-RNA attaches to the ribosome at the 5' end.
b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex.
c. A second t-RNA-AA binds to the second site
Phe
Meth
M-RNA:
G C A U G U U U G C C A A U
U G A

57. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
a. m-RNA attaches to the ribosome at the 5' end.
b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence, binds to the m-RNA/ribosome complex.
c. A second t-RNA-AA binds to the second site
d. Translocation reactions occur
Meth
Phe
M-RNA:
G C A U G U U U G C C A A U
U G A
The amino acids are bound and the ribosome moves 3-bases “downstream”

58. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
e. polymerization proceeds
Ala
Asn
Meth
Phe
M-RNA:
G C A U G U U U G C C A A U
U G A
The amino acids are bound and the ribosome moves 3-bases “downstream”

59. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
e. polymerization proceeds
Asn
Meth
Phe
Ala
M-RNA:
G C A U G U U U G C C A A U
U G A
The amino acids are bound and the ribosome moves 3-bases “downstream”

60. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
e. polymerization proceeds
f. termination of translation
Meth
Phe
Ala
Asn
M-RNA:
G C A U G U U U G C C A A U
U G A
Some 3-base codon have no corresponding t-RNA. These are stop codons, because translocation does not add an amino acid; rather, it ends the chain.

61. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
1. Transcription
2. Transcript Processing
3. Translation
4. Post-Translational Modifications
Meth
Phe
Ala
Asn
Most initial proteins need to be modified to be functional. Most need to have the methionine cleaved off; others have sugar, lipids, nucleic acids, or other proteins are added.

62. IV. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
C. Regulation of Protein Synthesis
1. Regulation of Transcription
- DNA bound to histones can’t be accessed by RNA Polymerase
- but the location of histones changes, making genes accessible (or inaccessible)
Initially, the orange gene is “off”, and the green gene is “on”
Now the orange gene is “on” and the green gene is “off”.