Download Week 3 Pre-Lecture Slides

Seminars in Bio200
•  The UW has hundreds of excellent public talks from top
scientists every quarter, but most students do not access this
unique resources until they are in their final year (if at all).
•  To help you step into the world of cutting edge science, we are
giving 30 points for completing this Seminar assignment. You’ll
need to:
–  Find a seminar that is likely to contain some Bio200 material
(anything with cells, genes, biotechnology, biomolecules, etc)
–  Go!
•  You won’t understand everything, and that is OK!
•  Try to relax and enjoy the experience
–  Afterwards, complete the Seminar Survey
•  You might want to take a look at this beforehand so you
know what you’ll be answering.
–  Due: Before the start of the last class of the quarter.
January 17th, 2016
Class 9 Learning Goals
Information Flow in the Central Dogma Model
•  After this class, you should be able to:
–  In broad terms, identify the movement of molecular information
–  Appreciate the historical significance in finding the molecular unit
of genetic information
–  Within the ‘Central Dogma’ model of genotype to phenotype:
–  Define and describe ‘transcription’
–  Define and describe ‘translation’
–  Identify potential phenotype-changing mutations in DNA
Peer Instruction
What are some examples of things that contain information?
How do you know?
Is information a physical thing?
Define ‘information’:
Peer Instruction
Coiled
1) What is supercoiling?
Supercoiled
DNA
•  One base pair = 0.34 nm (3.4E-9 meters)
•  Base pairs in the genome of each of
your cells: ~3 billion
2) Why is supercoiling important?
Supercoiled DNA
in chromosome
1. 
Define transcription:
2. 
Define translation:
3. 
Is transcription without translation useful in any way?
4. 
Is translation without transcription useful in any way?
5. 
Are all protein-coding genes read by the same cellular machinery?
6. 
The Central Dogma of Molecular Biology describes the most
common path of information flowing from a source into the design of
working molecules. Draw a simple diagram of the CDoMB:
Peer Instruction
Peer Instruction
3ʹ
5ʹ
5ʹ
3ʹ
5ʹ
3ʹ
Nʹ
Cʹ
Nʹ
Cʹ
5ʹ
3ʹ
Between these two alleles of the same gene:
•  Has the genotype changed?
•  Has the phenotype changed?
AGU CAU CAGACC GAAU CCGU ACG
UU AGG CAU
G C
GUA GUC UG
OH
• 
• 
• 
• 
• 
• 
• 
COO-
HN
Concept Questions
S
Why is DNA more likely to be the information storage molecule than RNA?
Why is protein more likely to be the working molecule than RNA?
Name two different ways that molecular information stored in the central dogma?
Without gaps, describe the progression of information from DNA to protein.
Define and describe ‘transcription’
Define and describe ‘translation’
In the given worksheets, identify and explain a potential phenotype-changing
mutation in DNA.
–  How is this mutation changing information?
–  Why is this mutation not guaranteed to change phenotype?
Peer Instruction
Proteins that should go to the Rough ER must be identified.
How does this information become encoded in the protein?
Cytosol
Ribosome
SRP
RNA
Signal sequence
Emerging Protein
Lumen of
rough ER
SRP receptor
Protein
Wednesday, January 18th, 2017
Class 10 Learning Goals
Transcription
•  After this class, you should be able to:
–  Label each molecule and strand (and give correct polarity for each
nucleic acid) in a diagram of a particular transcription
–  Predict and give a rationale for the effect of a loss-of-function
mutation in any component of prokaryotic transcription
–  Compare or contrast the three phases of prokaryotic trancription
(initiation, elongation, termination) in terms of enzymes and
substrates
–  Given a DNA sequence and promoter, predict the:
–  Direction of transcription
–  Polarity and type of the new molecule
–  Sequence of the new molecule
Transcription
Non-template
(coding) strand
Peer Instruction
DNA
RNA
5ʹ
5ʹ
3ʹ
3ʹ
Phosphodiester bond is
formed by RNA polymerase
after base pairing occurs
5ʹ
3ʹ
3ʹ
5ʹ
Template strand
RNA
5ʹ
3ʹ
Hydrogen bonds form between
complementary base pairs
DNA
template
3ʹ
What is “5’ to 3’ polarity”?
What is happening in this diagram?
5ʹ
1)  Label the 5->3 polarity of every strand.
Peer Instruction
2) Label the ‘template’ and ‘non-template’ strands
3) Label the ‘upstream’ and ‘downstream’ directions.
Peer Instruction
• 
Label the +1 site
• 
Where are – (minus) sequences numbered?
Peer Instruction
Label:
DNA molecule
Two different proteins
Label any:
Protein/DNA binding zones
Protein/protein binding zones
Peer Instruction
Label:
•  A region of DNA called the ‘promoter’
•  The enzyme called ‘RNA polymerase’
•  A small protein called ‘sigma’
•  What is a promoter?
• 
• 
What does sigma do?
Peer Instruction
Label the -10 box and -35 box and explain their names.
Label the upstream and downstream regions.
+1
• 
• 
• 
What has changed?
Label the +1 site
What are the yellow molecules?
Peer Instruction
Peer Instruction
• 
What changed from the previous diagram?
Rudder
Zipper
• 
What do the “zipper” and “rudder” do?
Peer Instruction
• 
• 
What is the transcription termination signal?
What is the yellow structure on the lower left?
Peer Instruction
Enzyme binding
to the termination hairpin
Two methods of
terminating transcription
‘Intrinsic’ disruption
by the new RNA itself
active site
•  The Transcription Problem:
Concept Questions
–  Create a stretch of double stranded DNA with random sequence
–  Flip a coin, and place the promoter to the left if heads (right if tails) and assume that the
promoter points the RNA polymerase towards the sequence in either case.
–  Flip the coin again, and put 3’ on the top right end of the strand if heads (5’ if tails).
–  Now: What is the new RNA molecule sequence and polarity?
•  What would happen to transcription if the -10 and -35 boxes were
switched? What if the +1 was a different base? What if the termination
sequence was lost?
•  There are four channels in the RNA polymerase protein leading from the
core to the outside. Name each of these channels usefully based on their
functions
•  Compare and contrast the three phases of prokaryotic trancription
(initiation, elongation, termination) in terms of enzymes and substrates
•  Transcription initiation starts right at the promoter. Why does termination of
transcription not occur until many bases after the termination signal?
Thursday January 19st, 2017
Class 11 Learning Goals
Translation
•  After this class, you should be able to:
–  Label each molecule and strand (and give correct
polarity for each nucleic acid and amino acid polymer)
in a diagram of protein translation
–  Predict and give a rationale for the effect of a loss-offunction mutation in any component of the ribosome
–  Compare or contrast the three phases of translation
(initiation, elongation, termination) in terms of enzymes
and substrates
Peer Instruction
An ‘adapter molecule’ is needed to hold amino acids
and interact with mRNA codons.
Amino
acids
Adapter
molecules
mRNA
Codon
Codon
Codon
Codon
Why didn’t transcription require an adapter molecule?
How many total adapter molecules are needed?
Because NTPs and dNTPs can directly forms base-pairs
Peer Instruction
1) What are the important parts of a Transfer RNA (tRNA)?
Binding site for the amino acid
3ʹ
5ʹ
3ʹ
5ʹ
3ʹ
mRNA
5ʹ
5ʹ
mRNA
3ʹ
2) How is a tRNA “charged”?
The machine that does translation: The Ribosome
tRNA in A site
(red)
Ribbon model of ribosome during translation
tRNA in E site
(blue)
tRNA in P site
(green)
Large
subunit
Small
subunit
Ribosomes catalyze peptide bond formation
Peer Instruction
How does this enzyme create a charged tRNA?
ATP
1)
3)
4)
2)
Activated
enzyme
complex
What parts of the enzyme give it specificity?
Concept questions
•  To practice labeling of translation diagrams:
–  Build a sequence with 70+ bases of random RNA
–  Find a start codon and assess the location of ribosome binding
–  Indicate the codons and anticodons used, as well as the peptide
bonds created
–  Change the sequence of the RNA such that you program the
ribosome to create a 10-amino-acid polymer
•  What would happen to translation if:
–  The ribosome binding site were lost?
–  The start codon were mutated?
–  The stop codon was mutated
–  The shape of the release factor was altered
•  Write a complete reaction diagram for each of these:
–  Binding of the small ribosomal subunit to the RNA
–  Addition of the 5th amino acid
–  Termination of translation
–  Catalysis of charging a single tRNA
Lab Next Week
•  The Central Dogma Lab
–  A great place to practice what you know about
•  Trancription
•  Translation
•  Mutation
–  We’ll also talk about mutations and their
impact on human disease for the first time