1. Inner Life of a Cell Inner Life Of A Cell - Full Version.mkv – YouTube
Music
Narrative: Harvard

2. Objective: To determine how proteins are made
Agenda: Nov. 26th
Homework: rDNA project due on Friday, Nov 30th
Pfeiffer Thank you notes due on Wed.
Objective: To determine how proteins are made
Warm up: Central Dogma
Proteins and how they are synthesized
Gene expression - review of process
Shape determines function
Senior Project Presentation
Tuesday: Proteins in more depth

3. Warm up:
What is the Central Dogma of Biology and Biotechnolgy?
Why is it important?

4. The CENTRAL DOGMA says:
DNA  _________ ___________
The first step will be to convert DNA to ______. This happens in the _______ and the process is called _____________.
Next, the _____ will be converted to a protein. This happens in the ___________ and the process is called ____________. This process will require assistance from the ___________ in the cell.

5. Transcription and
Translation

6. Inside a Cell
Journey Inside The Cell - YouTube

7. Protein structure and function
“Gene Expression”
Also known as “how to make a protein and how it works”

8. What do proteins do?
Each person has 30,000 different types of proteins and many millions of copies.
What is the function of proteins?
Notes for class notebook
Protein Functions in the Body – YouTube

9. The Structure of Life
Skim pages 6 – 9

10. Proteins are the body’s worker molecules

11. Proteins Structure determines function The Structure of Life
Or “proteins are shaped to get the job done”
The Structure of Life
Genetic Code p
Peering into Protein Factories p. 23
Beyond Drug Design pp

12. Proteins Structure determines function
Or “proteins are shaped to get the job done”
Examples:

13. Proteins – in muscles Myosin slides across actin

14. Antibodies – arm bind to foreign substance

15. Collagen Cartilage and tendons
3 strand, rope-like structure provides strength

16. Review
Base Pairing Rules for Transcription & Translation

17. Figure 14.5 Triplet Code
Each triplet of DNA bases codes for a triplet of mRNA bases (a codon), but it takes a complete codon to code for a single amino acid.

18. See p.12-13 Structure of Life for amino acid names & more details.
The Genetic Code

19. Amino acids form chains

20. Example of amino acids linked by polypeptide bonds (Note: protein synthesis has direction N to C)
Part of a protein: an opioid peptide that modulates the perception of pain

21. Codes for Amino Acids & Proteins

22. Enzyme: “Pencil transferase”
You will make a new protein (an enzyme) whose job (function) is to transfer a pencil.
Bend the pipe cleaner (chenille stems) so that a pencil can be moved from one table to another.
For the “pencil transferase” to function correctly, you cannot touch the pencil when moving it from your table to the next one.
Keep the successful shape. Draw it in your class notebook.

23. Questions:
Describe the shape of your protein. How would the shape change if one of the amino acids was eliminated?

24. Proteins –
shape determines function
Structure:
Primary
Secondary
Tertiary
Quaternary

25. Shape determines function
Primary structure
Order of amino acids
Combine to make proteins
Secondary structure
Alpha helix
Beta Sheet
Plus unstructured loops

26. Shape determines function
Tertiary
Globular: compact
Fibrous: linear
Quaternary
Multiple polypeptides (amino acid chains) come together

27. Read The Structure of Life
Agenda: Tuesday 11/27
Read The Structure of Life
The Genetic Code: pp
Worksheet: Genes to Polypeptides
Four Levels of Protein Structure
In more depth
Epigenome – When are proteins produced?

29. From Genes to Polypeptides
Complete worksheet

30. Figure 14.5 Triplet Code
Each triplet of DNA bases codes for a triplet of mRNA bases (a codon), but it takes a complete codon to code for a single amino acid.

31. See p.12-13 Structure of Life for amino acid names & more details.
The Genetic Code

32. Review: Protein Theater
Setting the scene:
Room walls are the cell membrane
Nucleus
Ribosome
Cytoplasm
Transcription starts with RNA polymerase recognizing a promoter
Gene on the DNA determines the complementary mRNA
mRNA specified the correct sequence for amino acids

33. Proteins Structure determines function The Structure of Life
Or “proteins are shaped to get the job done”
The Structure of Life
Genetic Code p
Peering into Protein Factories p. 23
Beyond Drug Design pp

34. Why do the amino acids fold in a certain way?

35. Differences in the amino acids
Resource:
Chem4Kids.com: Biochemistry:Twenty Amino Acids
Amino Acid Sequence of Bovine Insulin

36. Four Levels of Protein Structure
1. A protein’s primary structure is its amino acid sequence
Primary structure: the sequence of amino acids that form the polypeptide chains
A change in the primary structure can alter the resulting protein

37. Basic Amino Acid

38. 20 amino acids
Chem4Kids.com: Biochemistry:Twenty Amino Acids

39. Four Levels of Protein Structure
2. Secondary structure is polypeptide coiling or folding produced by hydrogen bonding
Secondary structure: parts of the proteins coil or fold into local patterns
Coiling: alpha helix
Folding: beta pleated sheets

40. Hydrogen bonds between amino acids
Backbones of the amino acids
C=0 attracted to the NH of the backbone another amino acid
Not the covalent bonds (peptide bonds)

41. Secondary Structure – Hydrogen Bonding
Alpha helix
Beta Sheet
(See                                                                                                                                            
other type.

42. Secondary shapes often combined into one 3-D structure called a domain Each domain has a function.
Note: Also unstructured loops
Note: Di-sulfide bridge
Strong covalent bond; acts as anchor

43. 3.Tertiary structure is the overall shape of a polypeptide
Tertiary structure: overall 3 dimensional shape of a protein
Globular: compact shape, enzymes
Fibrous: helical, tough, water-insoluble
Result of hydrogen bonding as well as ionic bonding (hydrophilic R groups)
Folded so that hydrophobic R groups are on the inside

44. Tertiary Structure: hydrophilic vs. hydrophobic R-groups
Amino Acid Structures

45. Basic Rules for Structure based on R groups
Hydrophobic
Hydrophilic
Non-polar
R groups with only C& H
Side chains fold up into the interior of the protein
Polar (ionic)
Attracted to water since water is polar
“Comfortable” in the watery environment of cytosol (cytoplasm)
Fold to be on the outside of the protein

46. Pipe cleaners Proteins: Shape determined by hydrophilic or hydrophobic
Choose:
4 pairs of smooth beads
4 pairs of triangle beads
String the beads in a random order
Triangle beads represent hydrophilic R-groups (same color attracted to each other)
Smooth beads represent hydrophobic R-groups and are in the interior of the protein
Fold the pipe cleaner protein to fit these rules
Draw the shape.

47. Pipe cleaner proteins
Compare your protein’s shape to others at your table.
How and why are they different?
What conclusions can you make about folding of proteins?

48. 4.Quaternary structure is the relationship among multiple polypeptides of a protein
Quaternary structure: when two or more polypeptide chains come together

49. Representing the structure of proteins
Protein in cell membrane:
Left: outside of membrane
Purple: where protein crosses
Right: inside of cell
Receptor protein: pass molecular messages from receptors to inside of cell

50. Major Unsolved Problem “Protein folding problem”
Scientists cannot predict shape & function of a protein based on the gene
Can determine the amino acid sequence
Can now make rough estimates of shapes
Compare to known proteins using data bases (bioinformatics)
Cannot accurately predict the position of each atom

51. Epigenome The Epigenome at a Glance Introduction – Nova
Video: Definition of Epigenetics - YouTube