Download Protein Structure

Do Now
• What happens to an egg when you fry it in a
pan? Why do you think this is? Explain using
your previous knowledge and experience.
• P. 31 of INB 2-3 sentences
Think About it
• How do you build a paragraph?
Build a protein
• On your desk, you have pipe cleaners and
ribbons
• You may twist, bend, curl your pipe cleaners
and ribbons
• You may make knots with the ribbon or make
small paper balls and push it through the pipe
cleaner
• You may not cut the ribbon or pipe cleaners.
Protein Structure
Today we will understand protein
structure and discuss how they are
made!
Build a Protein
• Why do proteins look like this?
• How do you think the shapes are formed?
• Can you try to undo your protein the way you
made it earlier?
Do Now
• Reflect on your test score: what could you
have done differently to better increase it?
What still confuses you? What do you need
most help on (study habits, note-taking, etc.)
• P. 35
Notes
• Rule of thumb for note taking
• Take note of anything bolded, underlined,
italicized it might be important later!
• Look at the HEADLINES of the slide so you
know what we’re currently discussing!
Protein Structures
• Know that there are 4 general levels of
protein structure
– Primary
– Secondary
– Tertiary
– Quaternary
• The first 3 levels are always present in
proteins
Primary Structure
• Is the direct product we get after translation
begins
– A polypeptide is a chain of amino acids
– This is the simplest level of protein structure
– These are linked together by peptide bonds.
• Made and broken by water
• Hydrolysis= water breaking
• Dehydration= water losing
Quick Build
• With your materials in front of you predict
what the primary structure of a protein might
look like
• Build using your pipe cleaners or ribbons or
both!
Primary Structure
No one is Always Right
• It is OK to be incorrect about predictions
• Scientists usually are a majority of the time
before they make a discovery
• Don’t be afraid to fail! It’s part of being a
scientist.
White-board quick check
• Write on your whiteboards answering these
questions: answer in either a drawing, a
definition, or a brief explanation
• How many levels of structure are there?
• What is the first level of structure called?
What does it kind of look like?
• How do you build the primary structure?
(think of the chemistry behind it).
Predict with a model
• What do you think the secondary structure of
a protein looks like?
• Work independently first then share with
your shoulder partner
• Use your materials and manipulate them in
what you think is right!
• Use the knowledge we just presented!
Secondary Structure
• This is the second level of protein formation
• It involves hydrogen bonds interacting with
each other
• The end outcome of hydrogen bond
interactions is a beta-pleated sheet or alpha
helix
• Loops, coils and sheets form from such
interactions.
White board Quick-Check
• Write a quick summary or draw an image on primary and
secondary structure
• Think about:
– Chemistry behind how these are made
– The best way to describe these structures
Whiteboard review
• How are proteins formed? Describe the
process in a concise paragraph using academic
vocabulary
• I will come check your responses.
Tertiary Structure
• Predict what you think the tertiary structure
might look like
• Think about what you already know from
primary structure. What else is there left to
do?
Tertiary Structure
• Is a 3-D shape that involves the R-groups of
the amino acids in the protein chain
• These side-chains interact with each other and
conform to form a 3D structure.
– Usually involves disulfide bridges, hydrogen
bonds, and hydrophobic interactions
Quaternary Structure
• Not always present in ALL proteins
• Usually involves 2 or more protein complexes that
come together due to bonds between adjacent
polypeptides
– This part of protein structure is “optional” and not always a
necessity when building proteins.
White-board Quick Check
• Draw, give a definition, or explain what the
tertiary structure looks like and how it is
formed.
• Summarize the key difference between a
quaternary structure and primary, secondary,
and tertiary structure.
Chaperone Proteins
• Chaperone proteins are involved in making
sure the protein folds in the correct way
– “hand holding” of polypeptide structure to make sure it
folds properly
– They stabilize partially folded regions in their correct
form
– Help chemical bonds form as the shape comes to be
– If something goes wrong, folding stops and more
chaperone proteins are transcribed to help with proper
folding.
#Tweet!
• On the poster in the front of the class
• Write a tweet (140 characters or less) on what
you think you learned about protein
structures
• Use #’s and @ and get creative!
Article Read
• Place the article on p.36 of your NB’s
• Answer the following questions on p. 35 below your Do
Now: complete sentences.
1. How are genetic disorders like PKU and amyloid neuropathy
caused?
2. What would a pharmacological (chemical) chaperone do in
this case?
3. What did the researchers do in order to test their chaperone
protein (summarize methods in your own words)
4. What can be a potential drawback to starting human trials?
What is the potential consequence?
5. How would scientists use proteins that are neither agonists or
antagonists? (mimic drugs vs blocks release of drugs in body)
Exit Ticket
• Please put away your notes
• Take time to do this exit ticket for 10 minutes
• Then We will switch and grade. Place graded
exit tickets on p.38
• You will write a reflection on your score!
Do Now
• What did you do over the weekend? How do
you like to spend time with your friends and
family?
• P.37
Today we will…
• Explain what happens to proteins when things
go wrong in the folding process
• How genes control which proteins are
expressed
• How cell specialization is determined
Protein Misfolding
• Misfolded Protein are sent out to the ER into
the cytoplasm, to be “tagged”
– Tagged by ubiquitin: a protein that is used on
misfolded proteins
– 1 ubiquitin allows for the protein to straighten out
and reform itself
– More than 1 ubiquitin tag: protein is sent out to a
proteasome mutli-protein structure used to
break down a misfolded protein!
Protein Misfolding
• Proteasomes also destroy proteins that are in excess and are
no longer needed.
– Allows for recycling of amino acids so they can be used again for other
proteins
– Also help to dismantle proteins from viruses
– Ex. Sickle-cell anemia is caused by improper forming of hemoglobin protein
– Can also cause “clogged proteasomes” when there is a disorder that
prevents proteasomes from breaking down proteins.
Whiteboard Quick Check
• Draw, describe in a paragraph, or write a
definition for what a proteasome is
• What occurs to a protein when it is misfolded?
Prions
• Prions cause diseases in the brain. These are glycoproteins
that are alternately folded
– One conformation is considered infectious, thus causing
another protein to change shape
– The diseases that prions cause are called transimissible
spongiform encephalopathies (TSE’s).
• Cause the brain to be full of holes
• Symptoms include tremors, dementia, and extreme weight loss
Mad Cow Disease
• Things like “mad cow disease” also formerly known as BSE
(bovine spongiform encephalopathy) are caused by feeding
infected organisms to cattle, which then ingest these
contagious prions
• Cruetzfeldt-Jakob Disease is a genetic disorder that causes
similar symptoms you would see in “mad cow”.
• Sometimes these disorders occur spontaneously with no
family history.
Summarize
• Read section 10.4 in your genetics text book and be sure to
answer the following questions after you have written a
summary on p. 37 of your notebook.
• 1. Build an acronym/short phrase to help you remember the
levels of protein structure
• 2. Draw a diagram that shows protein structure from primary
to quaternary: color and label diagram
• 3. Write a question you would ask on a quiz based on your
knowledge of protein structure:
– Make it highly rigorous if you feel extremely confident
(analyze, evaluate, predict, paraphrase, etc.) come see me
for key words for higher level questions.