Biology Standard 4A
DNA and Protein Synthesis
Cracking the Code Message
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___________________________________________________________
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Fall 2014
c-2 Ms. Darlak
Name: _______________________________
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Learning Targets
4A DNA & Protein Synthesis
I can identify the
structure of DNA
and how it pairs to
encode amino
acids.
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I can transcribe
and translate a
piece of DNA into
a protein.
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I can describe the
different types of
mutations.
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I can model the three subunits of a nucleotide.
I can model how DNA would replicate to create two semi-conservative strands.
I can describe and draw a double helix of DNA according to Chargaff's Rules.
Explain how Chargaff came to the conclusion about his rules and what evidence
was used.
I can describe the difference between DNA and RNA
I can transcribe a piece of DNA into mRNA.
I can translate a piece of DNA showing how mRNA, tRNA, rRNA and amino acids
are involved in the process.
I can recognize where to start and stop by the reading the codons.
I can explain how errors could be made in these processes.
I can recognize or describe what a point mutation is.
I can recognize or describe what a frame shift deletion mutation is.
I can recognize or describe what a frame shift insertion mutation is.
I can identify and explain which mutation is the deadliest if given examples.
Addition Mutation
Amino Acid
Codon
Deletion Mutation
Vocabulary
mRNA
Mutation
Protein
Ribose/Deoxyribose
Anti-Codon
DNA
Phosphate
Replication
Chargaff's Rules
Frameshift
Mutation
Point Mutation
RNA
2
rRNA
Transcribe
(Transcription)
Translate
(Translation)
tRNA
Erwin Chargaff and the History of Genetics
written by: Paul Arnold•edited by: Paul Arnold•updated: 11/7/2011
Erwin Chargaff (1905-2002), a gifted scientist in many fields, made several major contributions to the history of genetics. Rules that
were named after him laid the foundations for Crick and Watson's seminal paper on the structure of DNA.
Erwin Chargaff
Erwin Chargaff was working at Columbia University in New York in the 1940s when he read Oswald Avery's research about
DNA being the hereditary material. From that moment in 1944 he devoted his research to working out the chemical composition of
DNA. He commented on this many years later at a commemoration of 100 years of nucleic acid research. He said, "Avery gave us the
first text of a new language, or rather, he showed us where to look for it. I resolved to search for this text."
Chargaff's work is a vital part of the story of the history of genetics, not only because it shed more light on the function and
properties of DNA, but because it ultimately contributed to the groundbreaking work of Crick and Watson.
What are Chargaff's Rules?
His lab abandoned all other research and focused solely on DNA. At the time the tetranucleotide hypothesis was doing the
rounds. It said that DNA was made up of four bases (adenine, thymine, guanine and cytosine) that were present in regular amounts,
but that their organisation was too simple to carry hereditary information. It was Chargaff's work that overturned this.
By looking at the composition of DNA from various organisms i.e. plants, people and fish, Chargaff noticed that in any given species
the ratio of adenine to thymine was roughly equal, and the ratio of cytosine and guanine was also roughly equal. For example in
human DNA the ratios are; A=30.9%, T=29.4%, G=19.9% and C=19.8%. This rule is the same for every living thing. He had managed
to show that the chemical bases exhibited a complementary relationship.
Even though Chargaff made this discovery and published the research in 1950, the significance of these base-pairs (he did
not use that phrase) was to elude him. It wasn't until Crick and Watson's paper on the structure of DNA three years later that it was
fully understood. In fact they cited his work in their landmark paper.
One of his other major observations was that the composition of DNA varied from species to species, in particular the ratios of the
chemical bases.
Both these observations are now known as Chargaff's Rules, and it is likely that without them Crick and Watson's work
would not have been possible. In fact both did pay tribute to the debt they owed to Chargaff's research.
Reference
Source Chagraff's Quote: P and S Fall 2003; Vol 23, No 3
Reading Questions:
1. What was the tetranucelotide hypothesis?
2. What did Chargaff find that started to refute this hypothesis?
3
4
Reading Questions:
1. Linus Pauling published a paper right before Watson and Crick did on the Structure of DNA. What was
his hypothesis?
2. Why did Watson and Crick think that Pauling was wrong?
3. List 2 ways in that Watson and Crick’s model was different than Pauling’s model.
4. What did Watson and Crick claim as “novel” about their structure?
5. Watson says that if you know the sequence of bases on one side then _______________________
______________________________________________________________________________________
________________
6. Identify where Watson and Crick cite Chargaff’s rules as evidence for their paper:
7. Looking at the x-ray crystallographic image in Fig 1, of the models is supported by this photograph:
Linus Pauling’s 3-chain structure, or Watson and Crick’s 2 chain structure? Defend your answer.
5
DNA Notes
At the time most scientists believed that __________________ had to be the molecules that made up genes.
There were so many different kinds proteins (22!) and DNA seemed to be too monotonous ... repeating the same _____
subunits.
____________ _____________ At time no one knew why…
HERSHEY-CHASE BLENDER EXPERIMENT
Showed_______________ entered cell during infection.
Conclusion: ______________in virus was _____ not protein
STRUCTURE OF DNA – Double Helix
Discovered by _______________________________, and
___________________________.
AND ______________________ who never really got enough
credit.
NUCLEIC ACIDS are built from subunits called
___________________________________
SUGAR in DNA is _________________________.
DRAW:
Nitrogen Bases in DNA:
______________________ STRANDED
_________________________= A
Backbone (sides of ladder) made of
__________________ and ________________
_________________________ = G
_________________________ = C
_________________________ = T
CHARGAFF’s RULES _______________ ________________
At time no one knew why… now we know its because
DOUBLE HELIX
Adenine always bonds across with____________
____________________ bonds
between nitrogen bases hold
the two strands together.
Guanine always bonds across with ____________
http://www.hhmi.org/biointeractive/chargaffs-ratio
6
Nitrogen bases = “__________________________________________”
Make some DNA:
http://www.nobelprize.org/educational/med
icine/dna_double_helix/dnahelix.html
http://learn.genetics.utah.edu/content/begi
n/dna/builddna/
Chromosomes and DNA Replication
Prokaryote DNA is: _____________________________________________. Found in ______________________
Eukaryote DNA is:______________________________________________. Found in ______________________
When cell gets ready to divide, the fibers pack even more tightly to form ____________________________________.
(Makes it easier to move DNA during mitosis)
DNA Extraction Lab: http://www.pbs.org/wgbh/nova/body/extract-your-dna.html
http://learn.genetics.utah.edu/content/labs/extraction/howto/
HOW IS DNA COPIED?
The structure of DNA explains how it can be copied.
Each strand has all the info needed to construct the ______________________ other half.
If strands are separated,___________________________ rules allow you to fill in the complementary bases.
Sites where strand separation and replication occur are called ___________________________________________.
7
http://www.hhmi.org/biointeractive/dna-replication-basic-detail
http://www.lpscience.fatcow.com/jwanamaker/animations/DNA%20Replication%20-%20long%20.html
DNA Replication STEPS
1. Enzymes “unzip” molecule by breaking _______________ that hold the strands together and unwind it.
2.
____________________ joins nucleotides using original strand as template and __________________for
errors.
3. Copying happens in ______________ directions along the two strands & in _______________ places at once.
Thinking about it…
Name the 3 parts of a nucleotide molecule:
#1 = ____________________________
#2 = _____________________________
#3 = _____________________________
USING ANALOGIES:
If a double helix is compared to a “twisted ladder”, which would the following represent?
Sides of the ladder ? _________________________________
Rungs of ladder ? _______________________________
Glue in the middle that holds the two sides of the ladder together? ________________bonds.
Vocabulary:
__________________Enzyme that does the copying of DNA
__________________Location DNA is stored.
__________________ Name of the original strand of DNA
__________________ Name of the new DNA strand that is complimentary to the old one.
__________________ Name of the twisted and coiled DNA form that is ready to replicate. There are 23 of these.
__________________ Name of the form of DNA that it is normally in: wrapped in histones, but not coiled so
tight its ready to split the cell.
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RNA and Protein Synthesis Notes
Also made of _______________________. Sugar is ________________________ instead
of deoxyribose.
RNA is ___________________________ stranded. Contains ________________________
instead of thymine.
3 KINDS OF RNA HELP WITH INFO TRANSFER FOR PROTEIN SYNTHESIS
________________________RNA (rRNA) Combines with proteins to form ribosomes
____________________ RNA (tRNA) Matches m-RNA codon to add correct amino acids
during protein synthesis
___________________________RNA (mRNA) carries code from DNA to ribosomes
Transcription
Enzyme called _____________________ separates strands, then uses one
strand as a template to assemble an RNA copy.
How does it know when to stop?
Enzyme binds to places with specific DNA sequences called
____________________.
PROMOTERS tell ________________________ where to start. Signals at the
end of the gene code cause transcription to ____________.
RNA’s require EDITING before use
Animation:
http://www.hhmi.org/biointeractive/dnatranscription-basic-detail
http://sepuplhs.org/high/sgi/teachers/genetics_
act16_sim.html
Video:
http://media.pearsoncmg.com/bc/bc_0media_b
io/bioflix/bioflix.htm?cc7proteinsynthesis
https://www.youtube.com/watch?v=Ikq9AcBco
hA
http://www.stolaf.edu/people/giannini/flashani
mat/molgenetics/translation.swf
Practice:
http://learn.genetics.utah.edu/content/molecul
es/transcribe/
http://phet.colorado.edu/en/simulation/geneexpression-basics
https://www.youtube.com/watch?v=NJxobgkPEA
o
Why spend energy making a large RNA and then throw
parts away? May allow same gene to be used in
different ways in different kinds of cells. May have a
role in evolution… allows small changes in genes to
have a big effect.
http://www.hhmi.org/biointeractive/coding-sequences-dna
9
MASTER PLAN : DNA stays safe in nucleus
TRANSCRIPTION (DNA→ RNA) &
PROCESSING takes place in nucleus
TRANSLATION (RNA→ proteins) takes place on
ribosomes in cytoplasm
HOW CAN JUST 4 BASES GIVE DIRECTIONS TO MAKE 20 AMINO ACIDS?
Message is read in groups of 3 = _________
Codons represent different amino acids
UCGCACGGU
UCG-CAC-GGU
Translation
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FYI: When we
translate the
code using a
codon chart,
we always talk
about the code
on the mRNA
molecule, NOT
the anticodon
on the rTNA
molecule.
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Protein Synthesis Practice
Protein Synthesis Story:
•
Protein synthesis starts when (1.)____________________________ is opened by the enzyme
(2.)_________________________ which reads the nucleotides and creates a (3.)_____________________________
strand. This process is called (4.)________________________ and takes place in the
(5.)____________________________________.
•
Before a protein is made, the mRNA must (6.)__________________________________ and go to the
(7.)________________________ where three nucleotide (8.)____________________________ on the mRNA is
matched to the (9.)__________________ on the tRNA. Every time a tRNA is matched an
(11.)________________________ is added to the (12.)______________________ chain creating a protein. This
process is called (13.)_______________________ and it takes place in the (14.)_______________________.
WORD BANK:
Transcription
Codon
RNA Polymerase
Amino acid
Translation
mRNA
Anti codon
Nucleus
Leave the nucleus
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Polypeptide
Cytoplasm
Ribosome
DNA
Mutations NOTES
__________________________________ are changes in the genetic material.
Mutations can happen when cells make _____________ in copying their own DNA or be caused by _______________ or
___________ in the environment.
Mutations that produce changes in a single gene = ________________________________
Mutations that produce changes in whole chromosomes = ________________________________
Mutations involving ______________________________ ____________________________ =
____________________________ because they occur at a single point in the DNA sequence.
TYPES OF POINT MUTATIONS:
_______________________________
Piece of DNA code for a gene is lost
ATTCGAGCT
ATTGCT
Changes one base for another
ATTCGAGCT
ATTCTAGCT
_______________________________
Piece of DNA is copied too many times
ATTCGAGCT
ATTCTACTAGCT
_______________________________
Substitutions usually affect no more than a single _____________________________, but deletions and insertions can
have a more dramatic effect.
Frame shift mutations change every
_____________________ in the
_________________________ that follows the shift.
Frame shifts can alter a protein so much it is unable to
_______________________________
Location of the Shift is Important!
AT BEGINNING –Rewrite this phrase below without the t in
fat. –must all be in 3 letter chuncks!
the fat cat ate the rat
_________________________________________
AT END – rewrite without the last “e” in the sentence.
the fat cat ate the rat
_________________________________________
MUTATIONS AT _____________________________ OF GENE DAMAGE __________________________ OF THE CODE!
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The causes of mutations (Reading Assignment)
Mutations happen for several reasons.
1. DNA fails to copy accurately
Most of the mutations that we think matter to evolution are "naturallyoccurring." For example, when a cell divides, it makes a copy of its DNA —
and sometimes the copy is not quite perfect. That small difference from the
original DNA sequence is a mutation.
2. External influences can create mutations
Mutations can also be caused by exposure to specific chemicals or radiation. These agents cause the
DNA to break down. This is not necessarily unnatural — even in the most isolated and pristine
environments, DNA breaks down. Nevertheless, when the cell repairs the DNA, it might not do a
perfect job of the repair. So the cell would end up with DNA slightly different than the original DNA
and hence, a mutation.
Q1: Which of these causes of mutations do you think would have a greater effect on the
offspring of an organism and why? Defend your answer.
__________________________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
_____________________________________________________________________________________
The effects of mutations
Since all cells in our body contain DNA, there are lots of places for mutations to occur; however, some
mutations cannot be passed on to offspring and do not matter for evolution. Somatic mutations occur in
non-reproductive cells and won't be passed onto offspring. For example, the golden color on half of this Red
Delicious apple was caused by a somatic mutation. Its seeds will not carry the mutation.
The only mutations that matter to large-scale evolution are those that can be passed on to offspring. These
occur in reproductive cells like eggs and sperm and are called germ line mutations.
Effects of germ line mutations
A single germ line mutation can have a range of effects:
1.
2.
3.
No change occurs in phenotype.
Some mutations don't have any noticeable effect on the phenotype of an organism. This can
happen in many situations: perhaps the mutation occurs in a stretch of DNA with no function,
or perhaps the mutation occurs in a protein-coding region, but ends up not affecting
the amino acid sequence of the protein.
Small change occurs in phenotype.
A single mutation caused this cat's ears to curl backwards slightly.
Big change occurs in phenotype.
Some really important phenotypic changes, like DDT resistance in insects are sometimes
caused by single mutations. A single mutation can also have strong negative effects for the
organism. Mutations that cause the death of an organism are called lethals — and it doesn't
get more negative than that.
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Little mutations with big effects: Mutations to control genes
Mutations are often the victims of bad press — unfairly stereotyped as unimportant or as a cause of genetic disease. While many
mutations do indeed have small or negative effects, another sort of mutation gets less airtime. Mutations to control genes can have
major (and sometimes positive) effects.
Some regions of DNA control other genes, determining when and where other
genes are turned "on". Mutations in these parts of the genome can substantially
change the way the organism is built. The difference between a mutation to a
control gene and a mutation to a less powerful gene is a bit like the difference
between whispering an instruction to the trumpet player in an orchestra versus
whispering it to the orchestra's conductor. The impact of changing the conductor's
behavior is much bigger and more coordinated than changing the behavior of an
individual orchestra member. Similarly, a mutation in a gene "conductor" can cause
a cascade of effects in the behavior of genes under its control.
Many organisms have powerful control genes that determine how the body is laid
out. For example, Hox genes are found in many animals (including flies and humans)
and designate where the head goes and which regions of the body grow
appendages. Such master control genes help direct the building of body "units,"
such as segments, limbs, and eyes. So evolving a major change in basic body layout
may not be so unlikely; it may simply require a change in a Hox gene and the favor of natural selection.
Q2: Based on the reading, what do you think the word “Phenotype” means?
____________________________________________________________________
____________________________________________________________________
____________________________________________________________________
____________________________________________________________________
Mutations to control genes can
transform one body part into
another. Scientists have studied
flies carrying Hox mutations
that sprout legs on their
foreheads instead of antennae!
Q3: How can a mutation not cause any affect on the organism?
____________________________________________________________________
____________________________________________________________________
____________________________________________________________________
____________________________________________________________________
Q3: Explain how one mutation can affect many different genes.
__________________________________________________________________________________________________
__________________________________________________________________________________________________
__________________________________________________________________________________________________
__________________________________________________________________________________________________
__________________________________________________________________________________________________
Adapted from http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_05
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DNA WebQuest Review
10. Where does the first tRNA go?
Topic: Replication and Protein Synthesis
A. Go to:
http://www.pbs.org/wgbh/aso/tryit/dna/shockwave.html
Continue matching and answer questions.
Click: “DNA replication” (upper left) and then click “unzip”
11. How long will a real polypeptide chain get to be?
Read the script, answer the questions below, and then, click
“OK”.
1. In a real cell, what does the DNA molecule do before it
unzips?
12. When does translation of the mRNA end?
Topic: Protein Synthesis
2. What molecules break the rungs (bases) apart?
B. Go to:
http://learn.genetics.utah.edu/content/molecules/trans
cribe/
Drag the correct bases over to “synthesize” the new DNA
halves.
Click the button that says “click here to begin”
Read script, answer questions, and then click “OK”.
Use the keyboard to type the bases that would form the
mRNA. Follow the instructions to determine the order of the
amino acids.
3. How many base pairs are in the real human genome?
13. List the order of your amino acids.
Click “protein synthesis” (upper right). Click “upzip”.
4. How much of the DNA molecule actually unzips in a real
cell?
14. How did the process know to end?
Base pair the nucleotides for just one half of the DNA.
Read the script on the right side of the webpage.
Read the script, answer the questions, and click “OK”.
15. Describe the process of transcription.
5. About how many bases would a real mRNA molecule
have?
16. Describe the process of translation.
6. Where does the mRNA go now?
Match the tRNA molecules to their base pair nucleotides on
C. Go to: http://www.wisc-
the mRNA. Answer the questions.
online.com/objects/index_tj.asp?objid=AP1302
7. Which molecule has the codons?
Read the animation page by page – just click the “next”
button when you are ready to move on.
8. Which molecule has the anticodons?
17. How does the mRNA leave the nucleus?
9. What molecules are attached to the tRNAs?
18. Is just one mRNA molecule made? Explain.
Click “OK” and continue matching the tRNAs. Read the
script, answer questions, and click “OK”.
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19. How many amino acids does each codon code for?
37. How is DNA packaged to fit into the small space of a cell
nucleus?
20. Describe the structure of a tRNA molecule.
38. How many chromosomes are in a human cell?
39. Why are there “pairs” of chromosomes? Where do they
come from?
21. Where does the energy to form the peptide bond
between two amino acids come from?
40. Describe the sex chromosomes.
22. Can a single mRNA be read more than once? Explain.
Click on “What is a protein?” at the top and go through the
animation. Answer the questions.
Topic: Overview
41. What is the role of proteins in transmitting pain
messages?
E. Go to:
http://learn.genetics.utah.edu/content/basics/
42. Describe structural proteins.
Click on “What is DNA?” at the top and go through the
animation. Answer the questions.
43. “There are proteins involved in the making of proteins.”
Explain this sentence.
31. The complete set of instructions for making a human
being is found where?
Click on “What is heredity?” at the top and go through the
animation. Answer the questions.
32. What do genes tell the cell to make?
44. Give an example of the environment acting on the
expression of a genetic trait.
Click on “What is a gene?” at the top and go through the
animation. Answer the questions.
45. Where do we get our traits?
33. What is the function of the protein hemoglobin?
46. Explain how each child born to the same parents will
have a different combination of chromosomes.
34. How is sickle-cell anemia caused?
Click on “What is a trait?” at the top and go through the
animation. Answer the questions.
35. What are some other proteins that genes code for?
47. What are the different types of traits that can be
inherited?
Click on “What is a chromosome?” at the top and go through
the animation. Answer the questions.
48. Give an example of a physical trait that can be
influenced by the environment.
36. How long would the DNA in one human cell be?
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49. Give an example of a behavioral trait that can be
influenced by the environment.
51. How can two parents WITHOUT hitchhiker’s thumb have
a child who DOES have hitchhiker’s thumb?
50. Give an example of a predisposition to a medical
condition that can be influenced by the environment.
52. What is the definition of complex traits?
Topic: Mutations
F. Go to: http://evolution.berkeley.edu/evolibrary/article/mutations_03
Read the information and fill out the table below:
Type of mutation
Description
Effect on resulting protein
Substitution
Insertion
Deletion
Frameshift
Topic: Replication
G. Go to: http://nobelprize.org/educational_games/medicine/dna_double_helix/
Click on “Play DNA Game”; Click “next” and reading each page, continue to click next until you come to the game.; Click on organism #1 and
match the base pairs as fast as you can! It is hard. Click Next and then click on each organism until you identify the one that belongs to
chromosome #1; continue playing the game with the other two chromosomes, filling in the chart below. Be careful, other teams may get different
results.
Chromosome #
How many
chromosomes?
How many base
pairs?
How many genes?
1
2
3
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What is the
organism?
A bit of practice and review…
Compare and Contrast:
Double or single stranded?
DNA
RNA
Which sugar does it have?
List all nitrogen bases it has:
Which nitrogen base is it missing?
Where is it found in eukaryotic cells?
Match the mutation with its description:
______________________ Change in one or just a few nucleotides in the code.
Frameshift
______________________ Deletion or insertion that causes the reading frame on the remaining
nucleotides to be shifted over and read incorrectly.
Point
Dupilcation
______________________ One nucleotide in code is replaced by another.
Insertion
______________________ Piece of DNA is broken off and lost
Inversion
______________________ Piece of DNA breaks off, flips over, and reattaches backwards.
Deletion
______________________ Piece of DNA is added to the code.
Substitution
______________________ Extra copies of part of a chromosome are made.
Translocation
______________________ Piece of DNA breaks off and reattaches to another NONhomologous Chromosome.
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How much do you actually understand it? DRAW IT!
Draw DNA replication. Label steps, molecules, locations, and enzymes.
Demonstrate your knowledge of base pairs.
Draw protein synthesis starting with the DNA strand (CTGGCATACAGCCTATAGACCATCAG) and ending with
a polypeptide. Be sure to label all locations, processes, enzymes, and molecules. Demonstrate your knowledge
of base pairs, codons and anticodons along the way
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