1. Nutrition and Gene Expression Lecture, part 1, Feb 6, 2014 Overview: Gene Activation

2. WHAT IS A GENE? A gene is usually defined as sequence of DNA that codes for a protein. Control elements are also part the gene, and are critical to regulation of its expression The coding sequence is first read into an RNA sequence, which is processed to a message (mRNA). This is called TRANSCRIPTION. The mRNA is then read by ribosomes to make the protein. This is called TRANSLATION.

3. The basic structure of genes of course is DNA. Standard cartoon view View that shows base pairing

4. In a textbook, this strand is shown: “Coding strand” This is the “Template strand”, which is used to make an RNA copy. In this case, the Codon “CUA” will code for Leucine

5. HYPOTHETICAL SMALL CHROMOSOME: Double-stranded DNA, 1 million base pairs long CODING STRAND: template for RNA synthesis A B C D E These 5 genes (A-E) occupy only 100,000 base pairs (about (20,000/gene). The DNA in between has roles to be defined.

6. A B C D E Let’s focus on one gene, B. Region that is read into primary RNA transcript

7. ATGCTAATGTGCCTAT ATACGATGT CGCGTA TAATTGAT TACGATTACACGGATATATGCTACAGCGCATATTAACTA SIMPLIFIED STRUCTURE FOR A GENE Sequence to be copied into RNA Transcription factor binds here If there is a protein transcription factor to bind to the RED DNA SEQUENCE, then the GREEN SEQUENCE will uses as a template for a primary RNA transcript. THE STRANDS SEPARATE BEFORE RNA IS MADE!

8. WHAT IS TRANSCRIPTION? The synthesis of a complementary RNA strand, that matches the sequence of the DNA strand. This is the process where most regulation occurs, during gene expression. This will be illustrated with some very simple examples of this process.

9. DNA: TATACGATGTCGCGTATA RNA: AUAUGCUACAGCGCAUAU DNA: ATATGCTACAGCGCATAT Template strand: used by RNA-polymerase-II to make a complementary RNA copy Coding strand: If a textbook shows only one sequence, it will be this strand. It’s the same as the RNA transcript, except that the RNA has U instead of T.

10. Thymine (T) Uracil (U)

11. DNA: TATACGATGTCGCGTATA RNA: AUAUGCUACAGCGCAUAU During RNA synthesis: A pairs with T on the DNA U pairs with A C pairs with G G pairs with C Like DNA double strand, except RNA has U instead of T.

12. THE CORE QUESTION IN REGULATION OF GENE EXPRESSION – IS THERE A PROTEIN TRANSCRIPTION FACTOR TO START RNA SYNTHESIS? Otherwise, the DNA is usually not transcribed into RNA. In a typical cell, manyof the genes (about 60%) are hardly ever transcribed.

13. TRANSCRIPTION FACTORS THEMSELVES ARE PROTEINS. THESE PROTEINS FUNCTION TO ACTIVATE THE GENES THAT MAKE OTHER PROTEINS.

14. ATGCTAATGTGCCTAT ATACGATGT CGCGTA TAATTGAT TACGATTACACGGATATATGCTACAGCGCATATTAACTA EFFECTS OF BINDING OF SPECIFIC TRANSCRIPTION FACTOR (TF) A) TF protein binds to CONTROL SITE B) RNA Pol-II binds to the START SITE ATGCTAATGTGCCTAT ATACGATGT CGCGTA TAATTGAT TACGATTACACGGATATATGCTACAGCGCATATTAACTA Pol-II

15. ATGCTAATGTGCCTAT ATACGATGT CGCGTA TAATTGAT TACGATTACACGGATATATGCTACAGCGCATATTAACTA AU RNA SEQUENCE, COMPLEMENTARY TO DNA, IS MADE AS POL-II MOVES ALONG DNA SEQUENCE ATGCTAATGTGCCTAT ATACGATGT CGCGTA TAATTGAT TACGATTACACGGATATATGCTACAGCGCATATTAACTA AUAUGC ATGCTAATGTGCCTAT ATACGATGT CGCGTA TAATTGAT TACGATTACACGGATATATGCTACAGCGCATATTAACTA AUAUGCUACAGCGCAUAU

16. ATGCTAATGTGCCTAT ATACGATGT CGCGTA TAATTGAT TACGATTACACGGATATATGCTACAGCGCATATTAACTA Primary transcript made, ready for splicing and translation TRANSCRIPTION COMPLETE AUAUGCUACAGCGCAUAU NOTE: RNA-Pol-II will fall off the gene, and can then start transcription again.

17. For papers on genetics of fructose metabolism. FRUCTOSE INTOLERANCE: Lack of ALDOLASE causes fructose-1,6-diphosphate to accumulate

18. For discussion of the paper on hereditary fructose intolerance, we will review a database maintained on this disorder at Boston University: http://www.bu.edu/aldolase/HFI/hfidb/hfidb.html