1. From Gene to Protein
The Central Dogma

2. GENES determine traits by building individual proteins for that trait

3. An error in the gene = an error in the protein

4. The Central Dogma
DNA 
RNA
Amino Acid Chain (Protein)

5. 4. RNA can leave the nucleus, thus carries the "message"
Figure 14.3
DNA holds the instructions, while RNA carries out the instructions. RNA is a lot like DNA, except:
1. Ribose
2. Uracil
3. Single Strand
4. RNA can leave the nucleus, thus carries the "message" 

6. Each CODON specifies one AMINO ACID.
Figure 14.5
The instructions on mRNA (messenger RNA) are read by the ribosome as a series of 3 bases called a CODON
Each CODON specifies one AMINO ACID.
Some amino acids are repeated (third base wobble) to minimize mutations

7. The process where mRNA is made from DNA Follows base-pair rule
Figure 14.6
TRANSCRIPTION:
The process where mRNA is made from DNA
Follows base-pair rule
has uracil instead of thymine
RNA polymerase is used to build the strand of mRNA
Where have you heard the term “polymerase” before?

8. Transcription Animations
Transcription: Stolaf.edu
Transcription:  University of Nebraska
Transcription: Concord.org

9. Translation: process by which protein is built from the mRNA
Occurs at the ribosome (rRNA)
 tRNA brings amino acids to the developing protein chain
Each 3 bases on mRNA (called a codon) codes for a single amino acid by matching the anti-codon on tRNA

10. 3 bases on mRNA 
     = a codon
Matching 3 bases on tRNA
    = anticodon
Before translation begins, a tRNA must be “charged.” This ACTIVE process occurs when an enzyme attaches the appropriate amino acid.

11. Transcription (AP Level)
Transcription begins at the start of the gene called the promoter region. Enzymes bind to a “start” area called the TATA box. Each gene has its own promoter, so they cell can choose which genes to transcribe when.
After the enzymes are bound, the enhancer region (upstream from the start) trigger the enzymes to begin transcription. (This requires ATP.)
RNA polymerase unzips and copies the needed gene onto an mRNA strand until the termination sequence (end of gene) is reached.
The mRNA strand is then released, and the DNA rezips.

12. After Transcription
The mRNA must be edited before it can leave the nucleus and be used.
Introns (junk DNA) are removed, exons (needed DNA) are spliced back together by proteins called SNRPs. As a group, the SNRPs are called the Spliceosome.
A cap and a tail are added to protect the mRNA. Longer tails mean the mRNA can be used more often.

13. Alternative Splicing
Note: the same mRNA can be edited different ways. This alternative splicing allows the cell to modify the eventual protein being made and make different proteins from the same original mRNA template.

14. After Transcription comes…
TRANSLATION

15. Translation occurs on the ribosome in a series of steps.
1- initiation: the small subunit of the ribosome bonds to the start codon (AUG) of the mRNA. The appropriate charged tRNA (anti-codon UAC) links to the start codon. The large subunit of the ribosome attaches and the process begins. (If AUG is always the start codon, what is always the starting amino acid?)

16. Translation occurs on the ribosome in a series of steps.
2- elongation: the ribosome complex then moves along the mRNA reading each codon. New, appropriately charged tRNA molecules enter at the A site of the ribosome, release their amino acid to the growing polypeptide chain at the P site, and leave (un-charged without their amino acid) at the E site. Note: The un-charged tRNA can be recharged and reused

17. Translation occurs on the ribosome in a series of steps.
3- termination: When the ribosome reaches a stop codon, the entire complex releases and the created polypeptide chain begins protein folding. Note: Several ribosomes can translate the same piece of mRNA simultaneously to boost protein production.

18. * All genes start with AUG, also called the START CODON
amino acids
A U G
TRANSLATION (protein synthesis)
* All genes start with AUG, also called the START CODON
It attaches to anticodon UAC and the amino acid methionine.

19. This is the big picture. Can you explain it in your own words?

20. Animations of Translation
Translation: Stolaf.edu 
Translation: University of Nebraska
Translation: Concord.org

23. Regulation of Gene Expression

24. Consider that....
Every cell of the body contains ALL the DNA for the organism.
Not all genes are necessary all the time
Cells must have the ability to turn a gene on and off
ENTER:  THE OPERON MODEL 
OF GENE EXPRESSION

25. Operons and Gene Control
Experiments with E. Coli showed that it is capable of regulating the expression of its genes as gene sets called “operons”.
A prokaryote operon consists of the following elements
1.  Promoter   -  gene sequence where RNA polymerase attaches, signalling the start of the gene group
2.  Operator  -  where a repressor binds, stopping the transcription of that gene
3.  Structural Genes - genes coding for needed proteins, they are transcribed as a unit

26. The trp Operon
It controls the production of tryptophan, a necessary amino acid.
If tryptophan is already present, it binds to and activates the repressor to prevent more tryptophan from being made

28. The lac Operon (which produces lactase enzymes and helper proteins)
The lac Operon (which produces lactase enzymes and helper proteins). In this case, the prokaryote only needs lactase when lactose is present. This gene is essentially the reverse of trp in that the presence of lactose deactivates the repressor and turns on the gene.

30. REMEMBER!
Operons are only found in prokaryotes, but gene control in eukaryotes is similar. A little more complicated, but similar.

31. Repressors versus Inducers
The trp operon is a repressible operon, it is normally on but can be turned off when tryptophan is present. A repressor turns off a gene.
The lac operon is an inducible operon because it is normally off but can be turned on when lactose is present. An inducer turns on a gene.
Grammar Time
A woman is pregnant and the baby is later.  The doctor says they will "INDUCE" labor tomorrow.  What does he mean?

32. In eukaryotes, a variety of mechanisms regulate gene expression
1.  chromatin structure
2.  transcriptional control 3. post transcriptional control
4.  translational control
5.  post translational control

33. Chromatin Structure
Eukaryote DNA is wound around protein molecules called histones. More tightly wound regions cannot be reached for transcription. Less tightly wound are more easily accessed.
The others are pretty self-explanatory once you practice your vocabulary!

34. Chromatin Structure Example- BARR BODIES
In females, chromatin of one of the X chromosomes winds so tightly that it inactivates, this inactive chromosome is called a BARR BODY. This method of control can also be used in co-dominant pairs.

35. Barr Body in Cats

36. Genotype:     XB XO
The black patches are XB and the orange patches are XO, the cat is multicolored because not all X's are activated

37. Eukaryotic Gene Control
Transcriptional Control (stop/start transcription)
Post-transcriptional Control (modify the mRNA)
Translational Control (stop/start translation)
Post-translational control (modify the protein)
Remember that the cell is in control every step of the way. At any point, the cell can stop the process or modify the results of the process.

38. Gene Mutations
Point Mutations - single base changes, causing a change in the amino acid structure (protein); usually only one amino acid is changed.

39. Frameshift mutation
1-2 bases are added or deleted, shifting all codons downstream. This changes MULTIPLE amino acids in the protein.
G A T    C A T    A A A 
G A T    A  C A   T A A  A

40. Effect of Mutation on Protein
If the change results in replacement by the same amino acid (thanks to the third base wobble) and therefore a normal protein, this is called a “silent mutation” bc nothing actually changes.
If the change results in one single amino acid change, this is called a “missense mutation” bc the protein may still work, but not as before.
If the change results in multiple amino acid changes or a stop codon in the middle, this is called a “nonsense mutation”. Typically these proteins do not function at all.
Note: if a mutation can make a protein WORSE, it can also make it BETTER. The occasion of improved proteins are critical for evolutionary change.

41. What happens when you have a nonfunctional protein?
Hemophilia
PKU
Cystic Fibrosis
Etc.

42. Mutations and Cancer
If a TUMOR SUPPRESSOR GENE (Protein p53) is mutated, this often results in increased cancer risk.
When ONCOGENES (cancerous genes) activate, cell division occurs uncontrollably and tumors form
Example: Breast Cancer Gene
BRCA1  (pronounced brak-uh 1)