Inner Life of a Cell

• Inner Life Of A Cell - Full Version.mkv – YouTube

• Music

• Narrative: Harvard http://www.youtube.com/watch?v=GigxU1UXZXo&feature=fvwrel

Agenda: Nov. 26thObjective: 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

Homework: rDNA project due on Friday, Nov 30th

Pfeiffer Thank you notes due on Wed.

Warm up:

What is the Central Dogma of Biology and Biotechnolgy?

Why is it important?

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.

Transcription and Translation

Inside a Cell

• Journey Inside The Cell - YouTube

Protein structure and function

“Gene Expression”

Also known as “how to make a protein and how it works”

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• http://www.youtube.com/watch?

v=T500B5yTy58

The Structure of Life

– Skim pages 6 – 9

Proteins are the body’s worker molecules

Proteins

• Structure determines function– Or “proteins are shaped to get the job done”

The Structure of Life

• Genetic Code p. 12-13

• Peering into Protein Factories p. 23

• Beyond Drug Design pp. 52-55

Proteins

• Structure determines function– Or “proteins are shaped to get the job done”– Examples:

Proteins – in musclesMyosin slides across actin

Antibodies – arm bind to foreign substance

Collagen

• Cartilage and tendons– 3 strand, rope-like

structure provides strength

ReviewBase Pairing Rules for Transcription & Translation

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

Amino acids form chains

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

Codes for Amino Acids & Proteins

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.

Questions:

Describe the shape of your protein.

How would the shape change if one of the amino acids was eliminated?

Proteins – shape determines function

Structure:PrimarySecondaryTertiaryQuaternary

Shape determines function

• Primary structure– Order of amino acids– Combine 50-2000 to

make proteins

• Secondary structure- Alpha helix- Beta Sheet- Plus unstructured loops

Shape determines function

• Tertiary– Globular: compact – Fibrous: linear

• Quaternary– Multiple polypeptides (amino acid chains)

come together

Agenda: Tuesday 11/27

• Read The Structure of Life– The Genetic Code: pp. 12-13– Worksheet: Genes to Polypeptides

• Four Levels of Protein Structure – In more depth

• Epigenome – When are proteins produced?

From Genes to Polypeptides

• Complete worksheet

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

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

Proteins

• Structure determines function– Or “proteins are shaped to get the job done”

The Structure of Life

• Genetic Code p. 12-13

• Peering into Protein Factories p. 23

• Beyond Drug Design pp. 52-55

Why do the amino acids fold in a certain way?

Differences in the amino acids

• Resource:

• Chem4Kids.com: Biochemistry:Twenty Amino Acids

Amino Acid Sequence of Bovine Insulin

Four Levels of Protein Structure1. 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

Basic Amino Acid

20 amino acids

• http://www.personal.kent.edu/~cearley/PChem/amino/3d.htm

• http://wbiomed.curtin.edu.au/biochem/tutorials/AAs/AA.html

• http://www.chem4kids.com/files/aminoacids/index.html

• Chem4Kids.com: Biochemistry:Twenty Amino Acids

Four Levels of Protein Structure2. 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

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)

Secondary Structure – Hydrogen Bonding • Alpha helix • Beta Sheet

other type.

(See

                                                                                                                     

                      

Secondary shapes often combined into one 3-D structure called a domainEach domain has a function.

Note: Di-sulfide bridgeStrong covalent bond; acts as anchor

Note: Also unstructured loops

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

Tertiary Structure: hydrophilic vs. hydrophobic R-groups

• http://www.bio.davidson.edu/courses/genomics/jmol/aatable.html

• Amino Acid Structures

Basic Rules for Structure based on R groups

Hydrophobic

• Non-polar• R groups with only C& H • Side chains fold up into

the interior of the protein

Hydrophilic

• 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

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.

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?

4.Quaternary structure is the relationship among multiple polypeptides of a protein– Quaternary structure: when two or more

polypeptide chains come together

Representing the structure of proteins

Protein in cell membrane: Left: outside of membranePurple: where protein crosses Right: inside of cell

Receptor protein: pass molecular messages from receptors to inside of cell

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

Epigenome

• The Epigenome at a Glance

• Introduction – Nova

• Video: Definition of Epigenetics - YouTube