Summary comments: An essential pattern employed by all living things: DNA ö RNA ö Protein

Transcription

1 Summary comments: An essential pattern employed by all living things: DNA ö RNA ö Protein DNA is the information storage molecule. RNA in an intermediate in information flow. Proteins do most of the jobs in living things. What happens when a job doesn t get done? 1

2 M 109 Introduction I. PKU illustrates the relevance of chemistry to human health Why is chemistry important in human health? Ex.: PKU (phenylketonuria) ref. Matalon, KM Top lin Nutr 16(4):41-50 (2001) Blau, et al. Lancet 376: (2010) A. We are constantly being tested (from birth). 1) Why? Test newborns to check for congenital health problems. 2) What does congenital mean? 2

3 B. What is PKU? A genetic disease caused by insufficient phenylalanine hydroxylase (PA) activity. 1) PA rxn.: PA phenylalanine + oxidant tyrosine 2 O O 2 O + 3 N + 3 N 2) PA is an enzyme. (means? ) O - O - 3) The PA of PKU patients is absent or doesn t work as well as normal PA because its structure is different from normal, wild type (means? ), PA. This is 1 of ~ 10 4 jobs you must do to stay alive, healthy. 3

4 . Why does lack of PA activity cause problems in PKU? Note: Phenylalanine is found in foods containing protein. 1) Phenylalanine (Phe) levels increase. Some of this Phe is converted to phenylketones (excreted in urine). PA phenylalanine + oxidant tyrosine phenylketones 2) Part of the PKU pathology (means? ) appears to be caused by elevated Phe. ow Phe does this is not completely clear, (ex. :see Shefer, et al., J Neurosci Res. 61(5): , 2000). 3) Tyrosine (Tyr) isn t formed by the PA rxn in PKU patients. Tyr is an essential amino acid for them (diet supplements!). 4

5 Aside on PKU and diet Meat probably comes to mind 1 st when you think of protein in your diet, but most foods contain some protein. Some food additives also provide a risk for PKU patients. The structure of the artificial sweetener aspartame (found in some diet drinks) is shown below. Aspartame O O N+ N O O- O Why Aspartame might be a problem for PKU patients? Structure! 5

6 D. Back to Why test newborns? PKU can be treated! See: Irene, spouse, sister, (& Stephanie) (Pheno, Genotypes?) Put on your detective/diagnostician hat. What can you tell me about these 3 people? 6

7 Note: The pictures below and on the previous page are from The Montreal hildren s ospital yperphenylalaninemia (PKU) Resource Booklet for Families, by Peter M. Nowacki at The Biochemical Genetics Unit; updated by Annie apua, Margaret Lilly, David é, Manyphong Phommarinh and Shannon Ryan. Used with permission, Dr.. Scriver. 1. Set diet with low levels of Phe 2. Supplement w/ Tyr, which leads to healthy Irene & eventually to healthy 2 yr old Stephanie, þ E. What happens to PKU patients that are not treated or are not compliant with their treatment? i.e., What is the pathology? See Irene s sister, above. 1. Mental retardation (cause: high [phe]) 2. Microencephaly (means? ) 3. ongenital heart disease 7

8 F. Genetics Loss of function genetic diseases & diploidy. 0. A linear sequence of bases in your DNA that codes for a specific function is called a gene. 1. Genotype vs. phenotype (Look up if unfamiliar.) genotype phenotype 2. Why doesn t genotype = phenotype? Ploidy!!! a) Are you haploid or diploid? b) Better: i) Which of your cells are haploid? ii) Which of your cells are diploid? c) Now, are you haploid or diploid? This likely needs a longer answer. 8

9 3. What can you say re. genes of a PKU patient? Nice web site (from McGill Univ.) with lots of information about specific PKU mutations: also see: 4. What can you say re. genes of parents of a PKU patient? G. Like many medical/biological issues, the problem can get complicated because the PA gene is complex. It can go wrong, in many ways. (See figs & mutation map on following pages.) A major theme for this course, the entral Dogma: DNA ö RNA ö Protein 9

10 . ow does the entral Dogma relate to PKU & the PA gene? 1. From the uman Genome Project: haploid karyotype view. 10

11 2. Now search PKU There are different ways (mechanisms) to get PKU (important re. treatment strategies!). Our main interest is in the gene that codes for PA, which is on chromosome #12. 11

12 P A g e n e e x p r e s s i o n 3. Gene: a linear sequence of bases in DNA that codes (information) for a specific function (job). Fig. below based on: Dr.. Scriver, uman Mutation 28(9): (2007). PA gene expression DNA PA gene is 171,266 base pairs long Initial mrna Initial mrna ~ 170,000 basses long Mature mrna Mature PA mrna is 4,932 bases long 4,932 is ~ 2.9% of 171,266! Why have the extra 97%? PA Protein PA protein subunit is 452 amino acids long 12

13 Aside: It will be easier to understand if we relate the above processes to where they occur in a cell: What other kind of nucleus should you be able to draw? 13

14 4. The thin vertical lines in the mutation map (see link) ( are put together to form the mature mrna (short for? ). The open blocks labeled 1-12 are spliced out (& degraded?). 5. View the PA gene like a paper you have written that has 171, 266 letters. (Spelling errors possible?). Spelling error. a mutation (mutation: DNA sequence change). a) learly a spelling error could result in less effective communication. (like a harmful mutation) b) an you imagine a spelling error resulting in more effective communication. (a helpful mutation?) different mutations (as of )! PAdb website, Dr.. Scriver 14

15 I. If we understand, structure tells us about function and helps develop treatments. 1. The structure of DNA: a double helix (this piece is only 20 bp long!) space-filling model wireframe model ribbon model 15

16 2. Don t worry about RNA structure for now. 3. Structure of the protein PA (from PDB structure 1PA. ydrogen atoms are not shown. Object here is not to memorize atom locations.) Space-filling model, PK atom coloring Ribbon model. "-helices: red, $-sheets: yellow 16

17 J. Details of PA Mutations relate to patient treatment Imagine the PA molecule like a string of beads (452 beads long). You insert only one type of bead (of 20 total types available), and you always the same one (for w.t. PA) at each location: PA Sequence (partial) M S T A V L E Q K I K PA human amino acid sequence info from Kwok, et al., Biochemistry 24: (1985). The letters are the one letter code for one of the twenty common amino acids. M = methionine, S = serine, etc. Unless there is a mutation, position #1 is always M, #2 always S, and so on. Note: When you are making a completely different protein (for example, insulin) the sequence of that protein is very different that the amino acid sequence of PA. 17

18 Patient number 1 (a hypothetical, for simplicity s sake) Genotype: 290R'290R (Likely phenotype: full PKU) 0) Is this patient diploid or haploid? etero or homozygous? Odds of this phenotype occuring? 1) 290 means that the wild type gene codes for the amino acid histidine () at position 290 of PA. 290R means that a mutation is present in the gene, & the PA protein produced from this gene has an arginine (R) at position 290 of the PA protein. Later we will learn that this PA will have very little activity, and the patient must be treated with a strict low phe, high tyr diet (gene therapy?). PA Mutation 290R L G V P L G R V P Wild type gene produces this sequence in PA. mutation PA gene containing a mutation produces this sequence in PA. 18

19 Actual structural change: istidine side chain (wild type) Arginine side chain (in 290R mutant PA) O O N N 2 2 N 2 2 N N N +N We will learn later how changing only one amino acid out of 452 can have such a large effect on PA activity. 19

20 Patient 2 has the following genotype: I65T'R408W (Phenotype ranges mild to full PKU) From Erlandsen et al., PNAS 101(48): (2004) 0) Is this patient diploid or haploid? etero or homozygous? 1) I65: the wild type gene codes for the amino acid isoleucine (I) at position 65 R408: the wild type gene codes arginine (R) at position ) The patient received a chromosome with a mutation from one parent that yields a PA molecule with threonine (T) at position 65. The chromosome received from their other parent yields a PA molecule that is normal at position 65, but has a tryptophan at position 408. So, how many kinds of PA does this patient make? 3) The two types of PA molecules resulting from these mutations are the same as the wild type at all positions except 65 and 408, and these 2 mutant PA molecules do not show normal capacity to convert phenylalanine to tyrosine. Don t worry about the amino acid structures now. Later, we will. 1) What do these changes mean for the PKU patient? Important: this patient can undergo a better treatment than patient 1!!! 2) What change in the DNA would change the amino acid in PA from I to T? 20

21 K. By the end of the semester you should be able to: 1. predict what changes in the protein (PA) amino acid sequence will result from specific changes in the DNA base sequence (mutations) and 2. predict (in some cases) how specific amino acid changes in the PA sequence will alter PA activity. and 3. (sometimes) predict the best treatment for a given DNA mutation. 21

22 II. Administrative items A. Syllabus (posted on web /course structure 0. Introductions 1. Lecture (75% of grade) & lab/recitation (25%) 2. Attendance 3. Grading (what to do to succeed in M 109) 4. ivility B. Pace 1. Outside reading usually before lecture 2. Exams 3. Math issues (See web page!) 4. alculators for exams 22

23 . Re. previous recent M 109 classes: 1. Attendance 2. Deal w/ problems we have identified... before exams. 3. Your expectations vs. your ability & effort. 4. Passivity in lecture 5. Math issues (unusual semester?) 6. Pace relative normal academic year. (4 credits in summer = 12 credits in spring/fall semesters) If you have problems, are uncertain, etc., please see me!!!! Efficiently! 23