NUTRITION AND GENE EXPRESSION Jan 23, 2014 Dr. Garry Handelman DEFINITION OF A GENE

1. NUTRITION AND GENE EXPRESSION Jan 23, 2014 Dr. Garry Handelman DEFINITION OF A GENE

2. WHAT IS A GENE? From 1960-1980, it was defined as “the set of nucleic acids that code for a certain protein”. Each gene was known to have a specific chromosomal location. For example, during that period, the gene for the enzyme LDH was defined as the DNA sequence that specified the messenger RNA (mRNA) to make the protein LDH.

3. WHAT IS THE NEW DEFINITION OF A GENE? In the last 30 years, the gene was redefined. It includes the DNA that codes for the protein, AND the DNA that participates in the control of the activity of that specific gene.

4. THUS, AT TPYICAL GENE CONSISTS OF TWO COMPONENTS: • A CODING domain, that specifies the amino acid sequence • A REGULATORY domain, that participates in turning the gene on and off.

5. IN THIS COURSE, WE WILL DISCUSS BOTH THE CODING DOMAIN, AND THE PART OF THE GENE THAT IS INVOLVED IN REGULATION.

6. To understand the gene, consider the structure of DNA

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

8. 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 THIS RNA WAS MADE AS A COPY FROM THE DNA!

9. WHAT HAPPENS AFTER COMPLETION OF TRANSCRIPTION? The strand of RNA is usually processed to make a messenger RNA (mRNA). The mRNA is then read by ribosomes to make proteins. The genetic code specifies TRIPLETS on the mRNA which code for different amino acid.

10. Puffed-out region of DNA in Drosophila chromosome: INTENSE synthesis of RNA occurring

11. You will use these RNA triplet codons, for specific amino acids, for exercises throughout the semester.

12. For exercises on TRANSLATION of genetic code: amino acid side chains

13. THE CORE CONCEPT IN GENE EXPRESSION: SELECTIVE ACTIVITY OF GENES IN DIFFERENT TISSUES

14. MOST CELLS CONTAIN THE ENTIRE HUMAN GENOME – ABOUT 25,000 GENES THAT CODE FOR PROTEINS. THERE ARE TWO COPIES OF MOST GENES: A COPY FROM THE MATERNAL DNA, AND FROM THE PATERNAL DATA. • BUT – IN A TYPICAL CELL, ABOUT 10,000 GENES, ARE ACTIVE. THE REST OF THE GENES ARE DORMANT. THESE EXTRA GENE REMAIN IN THE NON-ACTIVE STATE. • THE CELL ONLY EXPRESSES THE GENES, AND MAKES THE PROTEINS, THAT IT NEEDS • THERE IS A NEW CLASS OF GENES THAT JUST MAKE REGULATORY RNA: WE WILL ALSO DISCUSS THIS AREA, BUT THE STATE OF KNOWLEDGE IS VERY EARLY

15. THE COMPLETE HUMAN GENOME: We will focus in this lecture on genes that are located on Chromosome 3

16. GENES IN CHROMOSOME 3 For illustration, we will discuss several different genes found on Human Chromosome 3: REMEMBER, YOU HAVE TWO COPIES OF THIS CHROMOSOME, AND GENES ON BOTH ARE USUALLY ACTIVE -A gene that is active in almost all tissues (pyruvate dehydrogenase, or PDH) -Another gene on Chromosome 3, only active in photoreceptors of the retina (rhodopsin) -Finally, a gene that is activated during fasting, when you burn fatty acids for energy (fatty-acid-CoA-ligase)

17. THESE GENES ARE UTILIZED TO DEMONSTRATE THREE KEY CONCEPTS IN GENE EXPRESSION: • Genes that are active, continually, in most cells • Genes that only operate in a very restricted set of cells, not affected by diet • Finally, genes that operate in a variety of tissues, and respond to dietary and other changes

18. PHOTORECEPTOR FIBROBLAST PDH GENE: ACTIVE IN MOST CELLS RHODOPSIN GENE: ACTIVE ONLY IN PHOTORECEPTORS FATTY-ACID-CoA-Ligase: Highly Expressed in Cells that Utilize Fatty Acids for Energy LIVER CELL, MUSCLE CELL

19. KEY CONCEPT: HOUSEKEEPING GENES These are genes that are active at all times, in all cells in the body. There are about 2,000 housekeeping genes. Examples: Na/K-ATPase – enzyme that pumps Na out, and K out, to maintain normal ion distribution inside the cell Pyruvate dehydrogenase (PDH): converts pyruvate to acetyl Co-A, at the entry point to the TCA cycle

20. GENES ON CHROMOSOME 3 Pyruvate dehydrogenase, beta-subunit: this gene is expressed in virtually all cells. A HOUSKEEPING GENE!

21. QUESTIONS: The PDH gene is shown on one copy of chromosome 3. • How many copies are there of this chromosome, in a typical cell? • Is the gene for PDH only active, on one copy of that chromosome?

22. QUESTION: -Is it necessary, for all the molecules of PDH in the cell to have the same amino acid sequence?

23. PDH complex (multi-protein): found in all cells that have mitochondria This complex, including the beta-subunit, converts PYRUVATE to ACETYL-CoA, which is then used in the TCA cycle, to make ATP.

25. KEY CONCEPT: TISSUE-SPECIFIC GENES These are genes that are only active in selected tissues, and remain dormant everywhere else. Examples: Globin gene: makes globin chain for Hb. Only expressed on red cell precursor cells in the bone marrow. Rhodopsin gene: produces key visual protein. Only expressed in rod photoreceptors of the retina.

26. GENES ON CHROMOSOME 3 Rhodopsin (main human visual protein): expressed only in rod photoreceptors. VERY TISSUE SPECIFIC. Cannot be expressed, except in the retina.

27. Rhodopsin is located in this part of the cell, and responds to light hitting the retina. NO OTHER CELL EXPRESSES THE GENE FOR RHODOPSIN! A ROD PHOTORECEPTOR CELL

28. KEY CONCEPT: GENES THAT RESPOND TO DIET These are genes that active in some tissues (not all), and which change with change in diet. THESE ARE THE GENES WE WILL STUDY IN DETAIL DURING THIS COURSE. Examples: TRPV-6 transport protein: up-regulated by calcitriol (the active metabolite of vitamin D); this protein is needed to absorb Ca(2+) from the digestive tract Fatty-acid-Co-Ligase: first step in beta-oxidation of fatty acids for energy, activated during fasting.

29. GENES ON CHROMOSOME 3 FATTY-ACID CoA LIGASE: This gene is activated when fatty acids are delivered to tissues for catabolism, such as during fasting. Can be expressed in heart muscle, skeletal muscle, liver, kidney. Its mRNA can also be decreased by high carbohydrate intake.

30. The conversion of fatty acids to CoA derivatives is catalyzed by: Fatty-Acid-CoA-Ligase To BETA-OXIDATION

31. REMEMBER, WE HAVE TWO COPIES OF CHROMOSOME 3! Pyruvate dehydrogenase, beta-subunit: this gene is expressed in virtually all cells. A HOUSKEEPING GENE! The PDH gene, beta-subunit is active at the same time on EACH chromosome (maternal and paternal): this protein is made from the PDH gene on each chromosome. As a general rule, both copies of each gene in your DNA are active (unless one copy is defective). If you have one good copy, usually it’s OK.

32. FOR CLASSROOM DISCUSSION: WHAT GENES WOULD YOU EXPECT TO BE ACTIVE IN THE FOLLOWING TISSUES? -WHITE CELLS -PANCREATIC BETA CELLS -CELLS THAT LINE THE STOMACH -PITUITARY GLAND

33. Since each cell only activates a PORTION of its total set of genes to make proteins – HOW IS THAT REGULATED? This is one of the fundamental questions addressed in human biology. The specific regulation of genes now consumes much of the effort in biology research.

34. THE STEPS IN PROTEIN SYNTHESIS. CONTROL CAN OCCUR AT EACH STEP IN THE PATHWAY!

35. RNA initially transcribed Processed to mRNA mRNA read into Protein Protein can be modified

36. MAKE THE INITIAL RNA PROCESS TO mRNA TRANSLATE TO PROTEIN MODIFY THE PROTEIN R

37. AS THE COURSE MOVES ON, WE WILL DISCUSS CONTROL OF EACH OF THESE FOUR STEPS WE WILL REVIEW IN DETAIL THE PATHWAYS OF GENE EXPRESSION. THIS BACKGROUND MATERIAL WILL HELP US TO UNDERSTAND GENE REGULATION.

38. YOU SHOULD BE MAKING A SERIES OF PROGRESSIVELY MORE DETAILED SKETCHES, AS YOU ADD INFORMATION TO YOUR MODEL OF GENE EXPRESSION AND THE GENOME