11 questions for a total of 120 points

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Morgan Elliott
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1 Your Name: BYS 201, Final Exam, May 3, questions for a total of 120 points points Take a close look at these tables of amino acids. Some of them are hydrophilic, some hydrophobic, some positive and some negatively charged (yes, it will depend on ph also, we will ignore that for now) Non Polar (hydrophobic) Polar (hydrophilic) Glycine Gly G Serine Ser S Alanine Ala A Threonine Thr T Valine Val V Cysteine Cys C Leucine Leu L Tyrosine Tyr Y Isoleucine Ile I Asparagine Asn N Methionine Met M Glutamine Gln Q Phenylalanine Phe F Tryptophan Trp W Proline Pro P Negatively charged (hydrophilic) Positively charged (hydrophilic) Aspartic acid Asp D Lysine Lys K Glutamic acid Glu E Arginine Arg Histidine His H Use this scoring scheme to align the two sequences you see in the grid. An exact match will have a score of 2, a like-like match (i.e. substituting a hydrophobic group for a hydrophobic group) will have a score of 1.0, a mismatch will have a score of -2.0, a gap penalty be I have given you two copies of this figure, in case you need it.

2 Question 1 continues... BYS 201, Final Exam, May 3, 2010 G L K L K F D K I G L H E K M Q D K I

3 Use it as need be and as it helps, the information and grid is on the same page Non Polar (hydrophobic) Polar (hydrophilic) Glycine Gly G Serine Ser S Alanine Ala A Threonine Thr T Valine Val V Cysteine Cys C Leucine Leu L Tyrosine Tyr Y Isoleucine Ile I Asparagine Asn N Methionine Met M Glutamine Gln Q Phenylalanine Phe F Tryptophan Trp W Proline Pro P Negatively charged (hydrophilic) Positively charged (hydrophilic) Aspartic acid Asp D Lysine Lys K Glutamic acid Glu E Arginine Arg Histidine His H G L H E K M Q D K I G L K L K F D K I 1

4 2. 20 points Consider the data in the three tables below. BYS 201, Final Exam, May 3, 2010 Normal Cancer Diabetes You are given the expression levels of 16 genes, in arbitrary units. Samples were obtained from normal individuals and those who had cancer or diabetes. The tables as you can see have 16 values each, in 4 rows and 4 columns. Each data point corresponds to the level of expression of a particular gene in each data set. You are told that when expression levels of a particular gene are at least 3 times of what is normal (or one third or lower of what is normal), that indicates a signficant difference in gene expression. Examine the data and identify which genes are expressed differently than normal for both cancer and diabetes. You must examine ALL possibilities, that is expression levels of ALL 16 genes. In the tables below enter ONLY those genes whose expression levels are significant.

5 Question 2 continues... BYS 201, Final Exam, May 3, 2010 Cancer Diabetes

6 BYS 201, Final Exam, May 3, points Consider the following four short protein sequences. As you may see, there are overlaps. Assemble ONE sequence from these four short sequences, taking into account the overlaps. GSGEADCG EADCG TFGSGEADCG 4. 5 points Consider the following four short nucleic acid sequences, assemble them into one taking into account any overlaps. ATATGCATGC ATGCAT GCATAAAA AATCTCGC

7 BYS 201, Final Exam, May 3, points You are given a solution that may have DNA, NA and proteins. Explain what experiments you would do, methods you will use to determine what is in the solution 6. 5 points Explain why embryonic stem cells can avoid transplant rejection 7. 5 points Explain the differences between embryonic and adult stem cells.

8 8. 5 points Explain what orthologs and paralogs are, in the context of genes. BYS 201, Final Exam, May 3, points Explain what shot gun sequencing is points Explain what PC is and briefly how it works.

9 BYS 201, Final Exam, May 3, points The partial gene sequence for a normal hemoglobin beta and a mutant variant are given below. Type Normal Mutant Sequence CTG ACT CCT GAG GAG AAG TCT CTG ACT CCT GTG GAG AAG TCT Write down the sequence of the amino acids each sequence codes for. Identify the mutant and why that mutation is critical for the gene. End of exam

Materials Protein synthesis kit. This kit consists of 24 amino acids, 24 transfer RNAs, four messenger RNAs and one ribosome (see below).

Materials Protein synthesis kit. This kit consists of 24 amino acids, 24 transfer RNAs, four messenger RNAs and one ribosome (see below). Protein Synthesis Instructions The purpose of today s lab is to: Understand how a cell manufactures proteins from amino acids, using information stored in the genetic code. Assemble models of four very