1. Cell Biology
I. Overview
II. Membranes: How Matter Get in and Out of Cells
III. Cellular Respiration
IV. Photosynthesis
V. Protein Synthesis

2. V. Protein Synthesis A. DNA/RNA Structure
DNA is the genetic material in all forms of life (eubacteria, archaea, protists, plants, fungi, and animals).
- genetic information (recipe for proteins)
RNA performs a wide array of functions:
- genetic information (copy of recipe)
- enzymatic function
- regulatory function

3. V. Protein Synthesis
A. DNA/RNA Structure
1. Monomers are “nucleotides” parts:
- sugar

4. V. Protein Synthesis
A. DNA/RNA Structure
1. Monomers are “nucleotides” parts:
- sugar, “nitrogenous base”

5. 1. Monomers are “nucleotides” - 3 parts: - sugar, “nitrogenous base”
V. Protein Synthesis
A. DNA/RNA Structure
1. Monomers are “nucleotides” parts:
- sugar, “nitrogenous base”
Nitrogenous base binds to the 1’ carbon

6. 1. Monomers are “nucleotides” - 3 parts:
V. Protein Synthesis
A. DNA/RNA Structure
1. Monomers are “nucleotides” parts:
- sugar, “nitrogenous base”, phosphate
Nitrogenous base binds to the 1’ carbon

7. 1. Monomers are “nucleotides”
DNA/RNA Structure
1. Monomers are “nucleotides”
2. Polymerization by dehydration synthesis OH OH
O-P-O O
H2O OH
Energy released by cleaving the diphosphate group can be used to power the dehydration synthesis reaction

8. DNA/RNA Structure
1. Monomers are “nucleotides”
2. Polymerization by dehydration synthesis
3. DNA strands are antiparallel and complementary

9. 1. Monomers are “nucleotides”
DNA/RNA Structure
1. Monomers are “nucleotides”
2. Polymerization by dehydration synthesis
3. DNA strands are antiparallel and complementary
4. RNA is made as a single strand, but can loop back
upon itself to make double-stranded regions.
A C G U A C A
U G C A U G A

10. Ribosomal RNA (r-RNA) is bound to proteins in a RIBOSOME
Messenger RNA (m-RNA) is a copy of a DNA protein recipe that is ‘read’ by a ribosome, and particular AA’s are linked together there. 5’ 3’
| | | | | | | | | | | |
A C G C C A U C U A C C …
Transfer RNA (t-RNA) attaches to free amino acids and transports them to the ribosome for polymerization into proteins

11. FUNCTIONS OF NUCLEIC ACIDS:
PROTEIN SYNTHESIS
CATALYZE REATIONS (RNA ONLY: “RIBOZYMES”)
REGULATION OF GENE ACTIVITY AND EXPRESSION
- TURNING GENES ON AND OFF
- REGULATING THE PROTEIN PRODUCT MADE FROM A GENE

12. VI. 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)

13. VI. 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

14. R-RNA is complexed with proteins to form ribosomes.
VI. 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

15. VI. 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

16. POST-TRANSLATIONAL MODIFICATION. (t-RNA) (r-RNA)
VI. 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

17. VI. 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

18. VI. 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!

19. VI. 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.

20. VI. 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).

21. VI. 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

22. VI. 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:

23. VI. 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:

24. VI. 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 by an RNA/protein complex called a ‘spliceosome’. Sometimes these reactions are catalyzed by the intron, itself, or other catalytic RNA molecules called “ribozymes”.

25. VI. 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.

26. VI. 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

27. VI. 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.

28. VI. 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

29. VI. 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

30. VI. 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”

31. VI. 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”

32. VI. 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”

33. VI. 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.

34. VI. 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.

35. mitosis Gene Regulation A. Overview
All cells in an organism contain the same genetic information; the key to tissue specialization is gene regulation – reading some genes in some cells and other genes in other cells.
zygote
mitosis

36. C. Regulation of Protein Synthesis
1. Regulation of Transcription
a. CHROMOSOME ARCHITECTURE
- 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”.

37. C. Regulation of Protein Synthesis
1. Regulation of Transcription
a. CHROMOSOME ARCHITECTURE
b. Proteins that REPRESSOR or INDUCE transcription (more tomorrow)
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
RNA POLY
Proteins can inhibit or encourage the binding of the RNA Polymerase. And, through signal transduction, environmental factors can influence the activity of these proteins. So cells can respond genetically to changes in their environment.

38. VI. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
C. Regulation of Protein Synthesis
1. Regulation of Transcription
2. Transcript Processing
intron
exon
Initial RNA PRODUCT:
G C A U GUUU G C C A A U
A UG A
C C C…
Proteins can bind to m-RNA and change splicing patterns.
This can turn protein synthesis off completely …. (here, a UGA is retained and stops synthesis prematurely…..)

39. VI. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
C. Regulation of Protein Synthesis
1. Regulation of Transcription
2. Transcript Processing
Or, a different combination of exons are spliced together…resulting in DIFFERENT PROTEINS produced from the SAME GENE.
A calcium regulator in the thyroid
Initial m-RNA
A hormone made in the brain

40. VI. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
C. Regulation of Protein Synthesis
1. Regulation of Transcription
2. Transcript Processing
Ds-RNA
intron
exon
Initial RNA PRODUCT:
G C A U GUUU G C C A A U
A UG A
U G A…
C G G U
Or, micro-RNA’s (mi-RNA’s) can bind to the m-RNA.
These are recognized by other enzymes and are cleaved incorrectly,
Or simply block the ribosome from translating the sequence.

41. VI. Protein Synthesis
A. Overview
B. The Process of Protein Synthesis
C. Regulation of Protein Synthesis
1. Regulation of Transcription
2. Transcript Processing
3. Regulating Translation
4. Regulating Post-Translational Modification
Meth
Phe
Ala
Asn
The patterns of cleavage and modification can vary.

42. PROCESS REGULATION GENE In DNA Transcription: DNA is read RNA is made
Chromosome architecture or protein binding enhances or represses RNA polymerase activity
2) RNA Splicing: Introns cut out
exons spliced together
Proteins binding to sites may enhance or inhibit spliceosome and change splicing pattern
3) Translation: Amino acids joined based on codon sequence in m-RNA
mi-RNA binding may stimulate incorrect splicing and m-RNA destruction, or block ribosome: no protein produced either way
4) Post-translational Processing:
Protein spliced; molecules added
Other enzymes present determine how the protein is modified
PROTEIN