Protein Synthesis: Making proteins

1. Protein Synthesis:Making proteins (Honors)

2. Why do cells need to make proteins? • Each protein has a specific structure to aid in cell processes – we have about 100,000 different proteins! • Enzyme : a protein with a binding site that matches up to ONE molecule (a substrate) that will allow the protein to make products • Helicase unzips DNA • ATP synthase makes ATP

3. Why do cells need to make proteins? • Each protein has a specific structure to aid in cell processes 2) Contractile Proteins: motion/movement (in your muscles) 3) Antibodies: fight foreign invaders in your body 4) Hormones: chemical messengers (like insulin) 5) Structural Proteins: support for connective tissue (collagen fibers) 6) Storage Proteins: store amino acids (like egg whites) 7) Transport Proteins: carrier proteins to move molecules from one place to another (protein = hemoglobin; job = carry oxygen)

4. DNA Contains the instructions to make Proteins

5. To make proteins, DNA and RNA are needed • DNA and RNA are both nucleic acids and genetic material • They differ in their structure and function

6. 3 Types of RNA • Messenger RNA(mRNA): carries genetic information from DNA in the nucleus to the cytoplasm • Transfer RNA (tRNA): folded in a hairpin shape, this binds to specific amino acids • Ribosomal RNA (rRNA): RNA nucleotides in globular form; this makes up the ribosomes where proteins are made

7. Transcription

8. Transcription = Making an mRNA strand in the nucleus using one DNA strand as a template • GENERAL INFORMATION: • mRNA is formed in the 5’ to 3’ direction, so new nucleotides always form on the 3’ end • When the DNA template has adenine (A), mRNA will have uracil (U) as the complement (not T) • RNA Polymerase unzips DNA and connects the new nucleotides to mRNA strand • Triplet nucleotides on mRNA are called codons (example : AAC is one codon, GGC another codon)

9. T A C C A T G A G A T T A T G G T A C T C T A A 1) INITIATION: An enzyme RNA Polymerase “unzips” DNA 3’ 5’ 5’ 3’ (Double Stranded DNA still intact)

10. T A C C A T G A G A T T A T G G T A C T C T A A Template Strand of DNA 3’ 5’ DNA

11. 2) ELONGATION: mRNA lengthens as the DNA strands continue to unwind • Begins at the promoters on the DNA – signal from DNA to RNA polymerase to start elongation here! • Free RNA nucleotides in the nucleus bind to exposed nitrogen bases by RNA Polymerase • DNA winds back up as mRNA is made

12. T A C C A T G A G A T T A U G first nucleotides on mRNA – AUG is the START codon 3’ 5’ 3’ 5’ A T G G T A C T C T A A

13. T A C C A T G A G A T T A U G G U A C U C U A A mRNA 3’ 5’ 5’ 3’ UAA, UAG and UGA are STOP codons that tell RNA Polymerase to stop transcribing DNA A T G G T A C T C T A A

14. 3) TERMINATION: Transcription continues until the RNA polymerase reaches a DNA region called the terminator sequence, which is a specific sequence of nucleotides that tells the RNA polymerase to stop! • mRNA transcript (strand) is released • DNA finishes winding back up • TRANSCRIPTION IS OVER! • UAA, UAG, and UGA are special sets of nucleotides that tell the RNA polymerase to stop adding nucleotides to the mRNA strand

15. Note, the code on the DNA is now on the mRNA but as a mRNA base pair- you could determine the sequence of DNA just by looking at this mRNA strand A U G G U A C U C U A A mRNA

17. A U G G U A C U C U A A codon codon codon codon The mRNA sequence from before can be broken up into CODONS Codon = A triplet of 3 bases on an mRNA strand

18. SPECIAL CODONS • AUG is a special codon-known as a start codon • It is a start signal that tells the ribosomes when to begin translation (the 2nd part of protein synthesis) • UAA, UAG, and UGA are special codons-known as a stop codons • They are signals that tells the ribosomes when to stop translation.

19. Completed mRNA…or almost complete  • At this point the mRNA strand is called pre-mRNA • The final mRNA is completely formed and ready to go to the ribosomes after… A) The addition of a 5’ cap and 3’ poly-A tail B) RNA splicing occurs

20. Addition of 5’ Cap and Poly-A Tail • Occurs after nucleotides are added during transcription to: • Help the mRNA get out the nucleus • Protect it from enzymes that want to EAT it up/break it down) • Attach the mRNA to the ribosomes for translation • Each end of the pre-mRNA is modified. • 5’ end= capped with a modified form of nucleotide guanine • 3’ end= after the stop codon, lots of adenine nucleotides are added (lots of adenine= Poly-A tail)

21. 5’ Cap and Poly-A Tail Image 5’ Cap Poly-A Tail Coded Segments= nucleotides added during Transcription

22. mRNA Splicing • Occurs after adding the 5’ cap and the 3’ Poly-A tail • mRNA Splicing= removal of large portions of RNA from the molecule that were originally added during transcription (i.e. mRNA cut and paste) • Introns= pieces of RNA that are removed or cut out of the original sequence • Exons= the remaining pieces of the sequence that are spliced/fused together – this code will be “expressed” in the protein • After exons are spliced/fused together= complete mRNA • Interestingly, sometimes introns from one round of transcription will be exons in another round…this gives us the ability to make about 100,000 different proteins from 25,000 genes mRNA now ready to leave the nucleus and go to the ribosomes for Translation!

23. Splicing taking place 5’ Cap Poly-A Tail 5’ Cap Poly-A Tail mRNA= Ready to go to the Ribosomes for Translation!

24. Translation

25. At the end of transcription, mRNA leaves the nucleus through a pore in the membrane and goes to the ribosomes in the cytoplasm

26. Ribosomes – structure and function …label cell now. Function: The site of protein synthesis; can occur freely in the cytoplasm or on the outer surface of rough endoplasmic reticulum (most common) Structure:made up of 2 subunits that aid in the production of proteins Large subunit Small subunit

27. Translation = converting an mRNA sequence into a short tRNA sequence to retrieve 1 of 20 amino acids to form a protein • GENERAL INFORMATION: • When mRNA has A, tRNA hasU and mRNA has U, tRNA has A • Occurs in the ribosomes • Cells can make 100s of proteins every second • Triplet nucleotides on tRNA are called anticodons (example : UUG) • 1st amino acid is always methionine (though often it is later removed) • Amino acids linked together = polypeptide chain = PROTEIN

28. tRNA = transfer RNA brings amino acids to the ribosome to be put together to form a polypeptide chain This anticodon would pair with the codon GUA on the mRNA Val

29. ser A G C Anticodon If this is the anticodon, what is the codon? Use the given codon chart to figure out the amino acid. A triplet on a tRNA

30. gly iso C C G U A U What is the codon? Why is the codon important? Anticodon on tRNA Anticodon on tRNA

31. A U G G U A C U C U A A • 1) INITIATION : a ribosome attaches to the mRNA strand at the start codon (AUG). • Imagine the ribosome is moving along the mRNA strand as we continue with each part of translation Ribosome will move Remember this mRNA?

32. met U A C A U G G U A C U C U A A 1) INITIATION (continued): The anticodon of tRNA pairs complementary to the AUG start codon on the mRNA and brings methionnine Anticodon: Which amino acid matches with it? Remember this mRNA?

33. met val U A C C A U A U G G U A C U C U A A 2) ELONGATION: (1st) as the ribosome moves along the mRNA strand, each codon is paired with its tRNA anticodon mRNA from before. What are the anticodons? Can you use the chart to find these AAs?

34. met val U A C C A U A U G G U A C U C U A A 2) ELONGATION: (2nd) peptide bonds are formed between amino acids as they arrive

35. met val leu G A G A U G G U A C U C U A A 2) ELONGATION: (3rd) as the next tRNA binds, the previous tRNA is released, leaving its amino acid behind mRNA from before. What are the anticodons? Can you use the chart to find these AAs?

36. met val leu A U G G U A C U C U A A A “polypeptide chain”= a protein

37. Another look at elongation Ribosome moving along mRNA

38. stop met val leu A U U A U G G U A C U C U A A 3) TERMINATION: a stop codon is reached (UGA, UAG, UAA); it does NOT code for an amino acid and the polypeptide is released

39. After a bit of rearrangement and folding, the protein is ready to perform its function (as an enzyme, a hormone, an antibody, structural support…see list) • Visit YouTube for many animations like this one: • http://www.youtube.com/watch?v=41_Ne5mS2ls

40. We’re almost done…Organelles involved in Protein Synthesis • Nucleus: mRNA is made from the DNA template in the nucleus • Ribosomes: tRNA attaches to mRNA and binds amino acids to make the protein • Endoplasmic Reticulum: what is that? • Golgi Bodies (Golgi Apparatus): what is that?

41. Rough Endoplasmic Reticulum (RER)- structure and function…label cell now. Function: allows protein synthesis to occur on a large scale due to many ribosomes packed on it • RER is responsible for transporting the newly synthesized proteins to the Golgi apparatus. Structure: layered curving area, presents a large surface area on which these ribosomes can be situated (rough endoplasmic reliculum)

42. Golgi Apparatus- structure and function…label cell now. Function: creates vesicles that transport carbohydrates to the protein chain to complete the process Structure: composed of flattened fluid-filled sacs that controls the flow of molecules in a cell by means of vesicles.