Review of Gene Expression Pathway in Cells

1. Review of Gene Expression Pathway in Cells GENE DNA mRNA copy of gene mRNA goes to cytoplasm Ribosomes translate genetic information encoded in the mRNA into protein building blocks (chains of amino acids) Protein folds into 3D active structure Protein functions in cell Focus on the Genetic Code!

2. Nucleus Executes The Genome Master Plan PLANT CELL: • Genome Master Plan is Executed: • DNA is copied into RNA code (mRNA) • (2)mRNA is transported to the cytoplasm • (3) Translate mRNA code into chain of protein building blocks at the ribosome. NUCLEUS CHLOROPLAST CELL WALL DNA (2) mRNA (1) (3) mRNA PROTEIN mRNA NUCLEAR PORE RIBOSOME CYTOPLASM CYTOPLASM CELL MEMBRANE Danny Schnell, BMB

3. Gene Expression: Pathway to Proteins • Genes Carry Instructions To Make Proteins: • DNA bases in each gene are copied into • mRNA code: A, G, C, T A, G, C, U • mRNA is sent to cytoplasm where ribosome translates mRNA code into protein chain. GENE 1 GENE 2 GENE 1 GENE 2 Protein 1 mRNA 1 mRNA 2 Protein 2

4. Controlling Gene Expression • The specific order of DNA bases in a gene encode • a protein product. • Genes have START and STOP signals that specify • the length of the protein chain. • Control DNA region is in front of the “coding region” • and controls expression of the gene. GENE Control DNA region is called a promoter. DNA region carrying protein information is called the coding region. +1 PROTEIN CODING REGION PROMOTER mRNA

5. Nucleus Executes The Genome Master Plan PLANT CELL: • How the Master Plan in the • Nucleus is Executed: • Copy the DNA code into RNA code, the (mRNA) • (2)Transport the mRNAout of the nucleus to the cytoplasm • (3) Translate the code in the mRNA into a protein molecule in a protein factory called a ribosome. NUCLEUS CHLOROPLAST CELL WALL DNA (2) (1) mRNA (3) PROTEIN mRNA NUCLEAR PORE RIBOSOME CYTOPLASM CYTOPLASM CELL MEMBRANE Danny Schnell, BMB

6. DNA Code Is Copied into a “Portable” Code: mRNA RNA POLYMERASE (RNAP: COPIES DNA INTO mRNA) DNA DNA U A C A A T T G Note: DNA base-pairs between backbone strands are not shown here 3’ mRNA mRNA: AUGGAGUACUAAUAUGUAAAAAAAAAAAAAAAAAAA-3’ DNA: ATGGAGTACTAATATGT-3’ TACCTCATGATTATACA-5’ MFHMAF2001

7. RNA Code has Different Alphabet Than DNA Code (RNA has U instead of T) DNA: ATGGAGTACTAATATGT-3’ TACCTCATGATTATACA-5’ 3’-TACCTCATGATTATACA-5’DNA STRAND AUGGAGUACUAAUAUGU mRNA copied from DNA DNA strand has “T” DNA Base-Pair RNA has U instead of T When DNA is copied into mRNA (transcription), U is incorporated into mRNA in place of T

8. DNA Strands “Unzip” so the DNA Letters Can be “Read” -ATGGAGTACTAATATGT- -TACCTCATGATTATACA- -TACCTCATGATTATACA- AUGGAGUACUAAUAUGU mRNA copied from DNA -ATGGAGTACTAATATGT- +AUGGAGUACUAAUAUGU mRNA -TACCTCATGATTATACA- DOUBLE-STRANDED DNA (Region from Chromosome) DNA STRANDS SEPARATE DNA STRANDS COME BACK TOGETHER BY BASE-PAIRING mRNA GOES TO CYTOPLASM TO PROTEIN FACTORY DNA HELIX STAYS IN NUCLEUS

9. Genetic Code is Written in 3-Letter DNA Words (Codons) -TACCTCATGATTATACA- DNA(DNA strands separated) -AUGGAGUACUAAUAUGU mRNA (copied from DNA) 5’-AUGGAGUACUAAUAUGU mRNA 5’-AUG GAG UAC UAA UAU mRNA mRNA code “read” by ribosome in TANDEM triplets called codons. Codon adaptors convert RNA letters into the correct amino acid building blocks in the protein chain. • CODON MEANINGS: • A “START PROTEIN” SIGNAL: AUG • A “STOP PROTEIN” SIGNAL: UAA, UGA, UAG • An amino acid building block of a protein • Codons identified in the Genetic Code Table

10. The Universal Genetic Code Table STOP Codons: UAA UAG UGA Name of Building Block Amino Acid: Phe=Phenylalanine Leu=Leucine Ile=Isoleucine AUG CODON: Signal to start making the protein. http://anx12.bio.uci.edu/~hudel/bs99a/lecture20/lecture1_6.html

11. N Met Glu Tyr C Genetic Code is Written in 3-Letter DNA Words -TACCTCATGATTATACA- DNA STRAND AUGGAGUACUAAUAUGU mRNA copied from DNA 5’-AUGGAGUACUAAUAUGU mRNA 5’-AUG GAG UAC UAA UAU mRNA Met-Glu-Tyr-STOP mRNA code is “read” in TANDEM CODONS A SHORT PROTEIN IS A PEPTIDE • CODON MEANINGS: • “START PROTEIN HERE”: AUG (START) Methionine (Met) • “STOP PROTEIN HERE”: UAA, UGA, UAG • Amino acid building blocks: N-Met-Glu-Tyr-C • Codons are identified in the Genetic Code Table

12. N Met Glu Tyr C Proteins Have Two Ends: The N- And C- Termini 5’-AUGGAGUACUAAUAUGU mRNA 5’-AUG GAG UAC UAA mRNA Met-Glu-Tyr-STOP A short protein (peptide) has only a few amino acid (aa) building blocks. The first aa in the chain (usually Met) (AUG) is at the N-terminus. The final aa added to the chain is the C-terminus.

13. Ribosome Protein Factory Reads the RNA Codons RNA is Copied From DNA (Gene) NUCLEUS GENE DNA UNZIPS mRNA Protein Synthesis Protein Chain Folds amino acid N AA Transfer RNA (tRNA): Matches mRNA codon with correct amino acid building block mRNA MFHMAF2001

14. PLAY DEXTER’S MOVIERibosomes and Protein SynthesisSee website for URL

15. Legend Hates Water Likes Water Likes Water Likes Water • Proteins live in a watery environment (living organisms!). • Chemical parts that hate water fold on inside of protein. • Chemical parts that love water go to the outside surface of protein. • Surface of the folded protein interacts with proteins, DNA, RNA, etc. Proteins Fold into 3D Structures Polar “Pocket” Small Folded Protein C N Hydrophobic “Pocket”

16. Different Protein Chains Fold to Make Proteinswith Different 3D Shapes and Biological Functions Protein #1 Protein #2 Protein #3 Protein #2 Protein #1 Human proteins have 20 different amino acid building blocks Protein #3

17. Molecular Structures Related to Protein Function in the Cell DNA Intersection: Holliday Junction EF Hand Binds Calcium Basket “Syringe” Channel

18. Spelling Mistake The DNA “word” TTC is changed to TTT A DNA Spelling Mistake Can Alter the Protein Chain START ADD ADD ADD ADD ADD ADD ADD STOP ATG TTC AGG CCA AAT TTT GTC GCG UAA GGA ATT ATG TTT AGG CCA AAT TTT GTC GCG TTC to TTT spelling change causes a different protein building block to be inserted in the second position. That is all it takes. ADD = Codon specifies the amino acid specified by 3-letter “word” ATG/AUG = Codon specifies start and methionine (met) UAA = STOP adding amino acids to protein chain

19. A Mutation is a DNA “Spelling Mistake” • Mutant Genes Encode Defective Proteins: • (1)WILDTYPE(2)MUTANT • Example: AAA GCT ACC TAT AAA GCT ATC TAT • TTT CGA TGG ATA TTT CGA TAG ATA • Phe Arg Trp Ile Phe Arg Stop • UAG • PROTEIN: WT FUNCTIONNO FUNCTION • (1) Normal DNA and amino acid sequence makes a wild-type protein. • (2) Mutation in DNA changes Trp to Stop to make a short, mutant protein. • Mutations in DNA can be Caused by: • Mistakes made when the DNA is replicated (wrong base inserted) • Ultra violet (UV) light and ionizing radiation (X-rays) damage DNA • Environmental chemical carcinogens can damage DNA • Other factors DNA Technology: The Awesome Skill, I E Alcamo, Harcourt Academic Press, 2001

20. X X Misspelled Genes: 3 Possibilities DNA A misspelled gene Cell may not be able to follow damaged instruction OR Damaged protein is made OR Spelling error may be harmless Damaged protein may or may not be able to function in the cell. Cell does not make the protein Functional protein made by the cell

21. Diseases Caused by Incorrect Protein Folding S. Hawking Charlton Heston Woody Guthrie Michael J. Fox Amylotropic Lateral Sclerosis Alzheimer’s Huntington’s Parkinson’s Slide from Dan Hebert, BMB (modified by K. Perry)

22. Complexity of Genetic Diseases Varies • Genetic diseases can involve one or more genes • Single gene diseases: • inheriting a single gene causes the disease • e.g., Huntington's Disease • Complex diseases involve interplay between • multiple genes • genes and environmental factors • e.g., heart disease, most cancers

23. What Causes DNA Mutations? • How Do My Genes Get Misspelled (Mutated?)? • 1.Inherit mutant gene from biological parents: • Genes from parents can have DNA misspellings • Many mutations are harmless • Some have consequences, whether mild or dire • 2.During the course of your life DNA Damage can be caused by: • UV radiation (Sunlight!!!) • Ionizing radiation (X-rays) • Environmental chemicals (pesticides, etc.) • Chemicals that bind to DNA (dyes, benzenes, etc.) • 3.Spelling mistakes in germ cells can be passed on to your children • NOTE: Your cells fight back with Protein Machines that locate and repair DNA damage! Some kinds of cancer are due to the failure of these proteins to properly repair DNA spelling mistakes!

24. Cystic Fibrosis (CF) Normal Dad (carrier) Normal Mom (carrier) • CF is a Genetic Disease: • 30,000 U.S. diagnosed/year • 12 million CF “carriers” in US: (Cc) • One CF gene (C) + one mutant • gene (cftr) (c) • Carriers (Cc): • Not sick, have one cftr gene. • Inherit one CFTR gene (C); and • one cftr gene (c). • CF Patients (cc): • Children are sick with CF. • Inherit one copy of mutant cftr • from each parent (two cftr(cc)). (cC) (Cc) Normal child (CC) Normal (carrier) (cC) Normal (carrier) (Cc) Cystic Fibrosis (cc) CFTR= CF transmembrane conductance regulator. CF inheritance is autosomal recessive.

25. CF is a Recessive Disorder This means that children will inherit the CF disease only if they inherit the mutated cftr gene from both parents. A gene called CFTR on chromosome 7 encodes an important protein that transports salt. There are two copies of chromosome 7 in every body cell and therefore two copies of the CFTR gene which codes for the protein which removes the salt. Both copies of the CFTR gene are mutated (cftr) in people with CF. Sometimes the altered CFTR gene that causes Cystic Fibrosis is called the CF gene.

26. Inheritance of Cystic Fibrosis Disease People have two copies of each gene. A person with a mutation in only one copy of the cftr salt-transport gene, will also have a correct CFTR gene and will produce enough of the salt-transport protein for normal body function. People who have one correct CFTR copy of the gene and one mutant cftr copy of the gene are called "carriers" of the mutation or genetic carriers. "Genetic carriers" of CF do not have cystic fibrosis because they can still produce enough salt-transporting protein to avoid having symptoms of the disease.

27. The Risk of Inheriting CF Depends on Your Parents If both parents are carriers of a cftr mutation there is a 25% chance (1 chance in 4), in every pregnancy, that they will have a baby who is affected with cystic fibrosis. However, if only one parent is a carrier of the mutated cftr gene, there is a 50% chance that their baby will be a carrier, and unaffected, but no chance that the baby will have cystic fibrosis. These risks apply to every pregnancy for this couple.

28. What Is The Mutation In The Salt-transport Gene That Causes CF? The most common mutation in the salt-transport gene, found in about 75% of CF people is called the F508 mutation. This means that one of the amino acid building blocks is missing in the cftr protein, because the codon for that amino acid is missing from the gene. There are also over 950 other rarer mutations which have been found at different places along the length of the CFTR gene.

29. How Is Cystic Fibrosis Detected? All newborn babies are screened for several inherited disorders including cystic fibrosis. A small blood sample is taken from the baby's heel in the first few days after birth and sent to a Newborn Screening Laboratory for analysis. An individual is at risk for being a carrier of a salt-transport gene mutation (a genetic carrier of CF) if there is a family history of cystic fibrosis or if a relative is known to be a genetic carrier of CF. There is a test to detect carriers of CF.