Download Structure and Function at a microscopic scale

Which choice completes this sentence?
“I throw my ________ up in the air
sometimes, sayin’ hey oh, gotta let go”
A) Books
B) Hands
C) Midterm
The 5 Big Ideas
Evolution
Viral Evolution
Evolution
Metabolism
Transfer of
Energy
Ecosystems
Systems
Endocrinology
Photosynthesis
Transfer of
Information
Structure
and Function
Animal Behavior
Cell Cycle
Organ
Structure
Molecular
Structure
The 5 Big Ideas
Evolution
Viral Evolution
Evolution
Metabolism
Transfer of
Energy
Ecosystems
Systems
Endocrinology
Photosynthesis
Transfer of
Information
Structure
and Function
Animal Behavior
Cell Cycle
Organ
Structure
Molecular
Structure
Structure and Function at a
microscopic scale
Katie Mouzakis
Bio375
Learning outcomes
• Design, or predict, and explain the
changes in Protein X’s structure and
function resulting from sequence
changes (a, b, c)
• Gene therapy- understand how changes
in protein function can result in disease
Discussion Question: Predict and explain the
changes in chymotrypsin’s structure and
function resulting from the following sequence
changes
Mutation
type
Sequence
change
Substitution AA 89: UUU →
UUC
Insertion
AA 89: UUU →
UUGU
Substitution AA 57: CAU
→AAU
Deletion
AA 101: AAC
→ AC
Change in
structure
Change in
function
Learning outcomes
To answer this question you need to
understand:
Relationships between protein sequence –
structure – function
What determines
protein function?
Protein structure!
Defn: Structure & Function
• Basic units of structure define the
function of all living things
Structure always dictates function
Eg. structure of your elbow joint dictates how you
can move your arm
This concept is true at all levels, and why structural
biology is incredibly useful!
Cellular are composed of a variety of structures,
many of which are made up of proteins & lipids
What are proteins?
I’m asking you!
Proteins are made up of (covalently)
linked amino acids
Question 1:
What are
proteins made up
of?
http://sun.menloschool.org/~dspence/biology/chapter3/chapt3_12.html
Amino Acids are Protein Building Blocks
All amino acids share
this core structure.
There are 20 natural
“R” groups, or
sidechains.
=
Sequence of amino acids defines the Primary Structure of a protein.
Amino acids are linked via peptide bonds
Amino Acid Side Chains (R groups) can be:
Hydrophilic
Polar
Charged
Hydrophobic
Nonpolar
Aromatic
e.g., Ser
e.g., Leu
e.g., Phe
e.g., Lys
Protein structures are dependent upon associations
water
between individual amino acids R groups
Fig 3-5, P. of Biochem.
Protein structures are stabilized by interactions
between amino acid side chains
Serine
Aspartate
Aspartate
Lysine
Valine
Isoleucine
Leucine
WoC Figure 3-5
Chymotrypsin
Example of protein structure &
function: Chymotrypsin
Chymotrypsin:
Substrate (a protein)
+ H2O
cleaves peptide bonds
adjacent to aromatic
amino acids residues
+
3
Fig 6-212a
Lehninger
P. Of Biochem
+
HO
Chymotrypsin & substrate
Empty chymotrypsin
Active site residues
Asp 102
His 57
Ser 195
Fig 6-212a
Lehninger
P. Of Biochem
Chymotrypsin & substrate
Chymotrypsin with substrate
Substrate (a protein)
+
Fig 6-212a
Lehninger
P. Of Biochem
Chymotrypsin structure
Side view
90°
Active
site
PDB ID 7GCH
Top view
Hydrophobic
pocket
Chymotrypsin structure
Top view
Active
site
PDB ID 7GCH
Hydrophobic
pocket
Hydrophobic
pocket
Question 2: Why is chymotrypsin specific
for peptide bonds when they are adjacent
to aromatic amino acids?
Why not after the other 17 amino acids?
Hydrophobic
AA interactions
Fig 3-5
P. Of Biochem
1 minute synthesis
Please take 1 min. to record/synthesize
what you just learned
If structure controls
function, what
controls structure?
Where do proteins come from?
Central Dogma of Molecular Biology
Reverse
Transcription
Remember
viruses
http://andersonlab.qb3.berkeley.edu/Tutorials/Basic_Molecular_Biology.htm
DNA to RNA
DNA
Transcription
RNA
5’ ... G C A U G C C U U A A A U G G C U G A U ... 3’
http://www.daviddarling.info/encyclopedia/G/gene.html
Reading the triplet code
RNA codons are a triplet of nucleotides that code
for an amino acid.
A U G = Methionine
e.g., C C U = Proline
Question 3
5’ ... A U G ... 3’
The first start codon establishes the reading frame
5’ ... G C A U G C C U U A A A U G G C U G A U ... 3’
Nucleotide triplets are read in a successive,
nonoverlapping fashion.
Using the RNA codon table we can
decode the sequence
3rd letter
Fig. 27-7
Lehninger,
Principles of Biochemistry,
4th Ed.
RNA is translated producing a chains of amino
acids
5’ G C A U G C C U U A A A U G G C U G A U ...3’
Translation
Met – Arg
RNA codon table activity
Question 4: Translate the following RNA
sequence
5’ ACGUGAAUGGUUAUGACAUAAUGA 3’
A) Met - Ser
B) Thr
C) Met – Val – Met - Thr
Modifying chymotrypsin function
How could you change its function?
A: change its structure
How could you change its
structure?
A: change its sequence
Change sequence
via mutation
Mutations in genomic sequence
Question 5: What is a mutation?
A change in nucleotide (N) identity
Mutation type e.g.,
Δ protein structure
Substitution
UUU → UUN varies
Insertion
UUU →
UNUU
Deletion
UUU → UU
Change in reading frame,
often results in encounter of
an early stop codon
Change in reading frame,
often results in encounter of
an early stop codon
Mutations and genetic disease
The structure and function of a protein can
change significantly if the sequence coding
for it changes.
This can have a large impact on cellular
function
What if a mutation occurs in a germ cell?
Guest speaker!
Natalie Salm
Achondroplasia
• The most common cause
of short stature
• 98% caused by a G to A
substitution at nucleotide
1138 in the FGFR3 gene
• Treatment is based on
the natural history of the
condition
– Examples:
• Sleep apnea
• Proper neck support
• Frequent neurologic exams
• Delayed motor development
Cystic Fibrosis
• Multi-systemic
– Pulmonary
– Digestive
– Reproductive
• Chronic illness with shortened life expectancy
• CFTR gene mutations prevent the proper flow of
salt and fluid in and out of the cell – causes sticky
mucous
• ~70% of cases due to a deletion of a single amino
acid, phenylalanine, at position 508 (deltaF508)
• 3rd most common mutation - G551D (~4%)
Cystic Fibrosis
• Kalydeco – first FDA
approved
medication for
patients with G551D
mutation
• Targets underlying
cause of CF
• ‘Unlocks’ the gate to
allow for normal flow
of salt
Fabry Disease
• Enzyme deficiency (a-galactosidase A) which is needed to
break down lipids
• Lack of this enzyme leads to harmful build up of lipids in
the eyes, kidneys, nervous system and cardiovascular
system
• Symptoms:
–
–
–
–
Periodic painful episodes
Cornea cloudiness
Increased risk of heart attack or stroke
Renal failure
• Treatment
– Enzyme replacement therapy ‘Fabrazyme’
Gene Therapy
Introduction of a gene
into a patient to treat
or prevent a disease.
• Clinical trials
• Pros – cure?
• Cons – formation of
new problems?
Medical
enhancement vs.
medical treatment
Providers
Multidisciplinary Teams
• Clinical Geneticists
• Genetic Counselors
• Nurses
• Dieticians
What we do:
• Review family history
• Physical evaluation
• Discuss testing
options
• Propose a diagnosis
• Help with long term
management
To find more information on genetic counseling visit
www.nsgc.org
Genetics in Wisconsin
http://www.slh.wisc.edu/genetics/index.dot