1. Molecular Biology of the Gene DNA Structure and Function
Chapter 10
Molecular Biology of the Gene
DNA Structure and Function

2. History of DNA 1869 Johann Friedrich Miescher
1924 Microscope studies using stains for DNA and protein show that both substances are present in chromosomes.
1952 Alfred Hershey and
Martha Chase

3. 10.3 SCIENTIFIC DISCOVERY: DNA is a double-stranded helix
Erwin Chargaff
Rosalind Franklin / Maurice Wilkins
James Watson and Francis Crick
In 1962, the Nobel Prize
Student Misconceptions and Concerns
Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. The authors note that the structure of DNA is analogous to a twisted rope ladder. In class, challenge your students to explain what the parts of the ladder represent. The wooden rungs represent pairs of nitrogenous bases joined by hydrogen bonds. Each rope represents a sugar-phosphate backbone.
© 2012 Pearson Education, Inc. 3

4. 10.1 SCIENTIFIC DISCOVERY: Experiments showed that DNA is the genetic material
Until the 1940s, the case for proteins serving as the genetic material was stronger than the case for DNA.
Proteins are made from ____different amino acids.
DNA was known to be made from just ____ kinds of nucleotides.
Studies of bacteria and viruses
ushered in the field of molecular biology, the study of heredity at the molecular level, and
revealed the role of DNA in heredity.
Student Misconceptions and Concerns
1. Understanding bacteriophage replication can be difficult for students with limited knowledge of cell biology or genetics. Therefore, understanding the methods, results, and significance of the Hershey and Chase experiments is even more problematic. Considerable time and attention to these details will be required for many of your students.
2. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
Teaching Tips
1. A phage functions like a needle and syringe, injecting a drug. The needle and syringe are analogous to the protein components of the phage. The drug to be injected is analogous to the phage DNA.
2. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
© 2012 Pearson Education, Inc. 4

5. 10.2 DNA and RNA are polymers of nucleotides
DNA and RNA are nucleic acids.
The building blocks or monomers of nucleic acids are ____________________
A nucleotide is composed of a
_________________
__________________
The nucleotides are joined to one another by a bond creating the sugar-phosphate backbone.
Student Misconceptions and Concerns
1. If your class has not yet studied Chapter 3, consider assigning module 3.15 on “Nucleic Acids” before addressing the contents of Chapter 10.
2. Students often confuse the terms nucleic acids, nucleotides, and bases. It helps to note the hierarchy of relationships: nucleic acids consist of long chains of nucleotides (polynucleotides), while nucleotides include nitrogenous bases.
Teaching Tips
1. The descriptions of the discovery of DNA’s structure are a good time to point out that science is a collaborative effort. Watson, Crick, and Wilkins earned Nobel prizes due to their historic conclusions based upon the work of many others (including Franklin, Griffith, Hershey, Chase, and Chargaff).
2. Consider comparing DNA, RNA, and proteins to a train (polymer). DNA and RNA are like a train of various lengths and combinations of four types of train cars (monomers). Proteins are also “trains” of various lengths but made of a combination of 20 types of train cars.
© 2012 Pearson Education, Inc. 5

7. Sugar-phosphate backbone
Phosphate group A T G C A A G
Nitrogenous base
Nitrogenous base (can be A, G, C, or T)
Covalent bond joining nucleotides A T G C
Sugar T A C C T A C C C G T A
DNA nucleotide
Thymine (T)
A DNA double helix T T T
Phosphate group
Figure 10.2A The structure of a DNA polynucleotide G G
Sugar (deoxyribose)
DNA nucleotide G G
Two representations of a DNA polynucleotide 7

8. 4 Different Types of Nucleotides Found in DNA

9. Partial chemical structure
Figure 10.3D
Hydrogen bond
Base pair
Figure 10.3D Three representations of DNA
Ribbon model
Partial chemical structure
Computer model 9

10. 3’ and 5’ ends to nucleotide strand….

11. Purine or pyrimidine ?
Hydrogen bonds hold the 2 strands together

12. 2 General Functions for DNA1. 2.
Replication
DNA makes an exact copy of itself during the S phase of the cell cycle (before mitosis or meiosis)
Every cell must have a complete copy of “instructions”
Protein Synthesis
Genes contain the instructions for building specific proteins
The interaction of genes allows for the expression of traits

13. 10.4 DNA replication depends on specific base pairing
In their description of the structure of DNA, Watson and Crick noted that the structure of DNA suggests a possible copying mechanism.
DNA replication follows a semiconservative model.
__________________________________________
Student Misconceptions and Concerns
The two DNA strands separate.
Each strand is used as a pattern to produce a complementary strand, using specific base pairing.
Each new DNA helix has one old strand with one new strand.
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. Demonstrate the complementary base pairing within DNA. Present students with the base sequence to one side of a DNA molecule and have them work quickly at their seats to determine the sequence of the complimentary strand. For some students, these sorts of quick practice are necessary to reinforce a concept and break up a lecture.
2. The semiconservative model of DNA replication is like making a photo from a negative and then a new negative from the photo. In each new negative and photo pair, the new item was made from an old item.
© 2012 Pearson Education, Inc. 13

14. A parental molecule of DNA
Figure 10.4A_s3
A T T A A T
A T
A T
C G C G G
C G
C G C
G C G C C
G C
G C A
A T A T
A T
A T
Free nucleotides
T A T A
T A
T A
A parental molecule of DNA
The parental strands separate and serve as templates
Two identical daughter molecules of DNA are formed
Figure 10.4A-s3 A template model for DNA replication (step 3) 14

15. 10.5 DNA replication proceeds in two directions at many sites simultaneously
DNA replication begins at the origins of replication where
DNA unwinds at the origin to produce a “bubble,”
replication proceeds in both directions from the origin, and
replication ends when products from the bubbles merge with each other.
DNA replication occurs in the 5 to 3 direction.
Replication is continuous on the 3 to 5 template.
Replication is discontinuous on the 5 to 3 template, forming short segments.
Student Misconceptions and Concerns
DNA unwinds at the origin to produce a “bubble,”
replication proceeds in both directions from the origin, and
replication ends when products from the bubbles merge with each other.
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask the students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter.
2. There are about 500,000 words in the Biology: Concepts & Connections textbook. The accuracy of DNA replication would be like copying every word in this textbook by hand 2,000 times and writing just one word incorrectly, making one error in every 1 billion words. 15

16. Leading and Lagging strands
Why?
DNA polymerases can only assemble new strands in the 5’-> 3’ direction, need a 3’ end
(-OH) provided by RNA primer.

18. DNA polymerase molecule
Figure 10.5C 3
DNA polymerase molecule
This daughter strand is synthesized continuously 5
Parental DNA 5 3
Replication fork
This daughter strand is synthesized in pieces 3 5
Figure 10.5C How daughter DNA strands are synthesized 5 3
DNA ligase
Overall direction of replication 18

19. 10.5 DNA replication proceeds in two directions at many sites simultaneously
Key proteins are involved in DNA replication.
Helicase
DNA Polymerases-
Primase
Proofreader
DNA ligase
Student Misconceptions and Concerns
Helicase breaks H bonds that hold nucleotide strands together.
DNA Polymerases catalyze the formation of the two new strands of DNA from free nucleotides, also proofread strands.
DNA ligase bind Okazaki fragments together
Only can assemble in the 5’-> 3’ direction
One strand has continuous replication, while the other is discontinuous
Nucleotide “starter” needed:RNA primase creates RNA primer to get polymerization started.
The authors note that although the general process of semiconservative DNA replication is relatively simple, it involves complex biochemical gymnastics. The DNA molecule is unwound, each strand is copied simultaneously, the correct bases are inserted, and the product is proofread and corrected. Before discussing these details, be sure that your students understand the overall process, what is accomplished, and why each step is important.
Teaching Tips
1. To explain the adaptive advantage of multiple replication sites over a single site of replication, ask the students to imagine copying, by hand, the first ten chapters of your biology textbook. The task would certainly go faster if ten students each copied a different chapter.
2. There are about 500,000 words in the Biology: Concepts & Connections textbook. The accuracy of DNA replication would be like copying every word in this textbook by hand 2,000 times and writing just one word incorrectly, making one error in every 1 billion words.
© 2012 Pearson Education, Inc. 19

20. Two daughter DNA molecules
Figure 10.5A
Parental DNA molecule
Origin of replication
Parental strand
Daughter strand
“Bubble”
Figure 10.5A Multiple bubbles in replicating DNA
Two daughter DNA molecules 20

21. Animation: Origins of Replication

22. Animations- DNA REPLICATION
The above animation shows a few additional enzymes
A few extra details are shown.

23. Animation: Lagging Strand

24. Animation: DNA Replication Review

25. DNA Repair Mismatches occur typically once every 10 thousand to
1 million additions.
A type of DNA polymerase can fix pairing errors
Other repair enzymes can repair DNA changes (breaks in backbone, bonding between bases in same strand or to more than one base in complementary strand) by clipping out “bad” parts and correcting.
If repair cannot be made often the cell can be programmed for “death” rather than keep a mutation

26. DNA processes
Replication
Protein Synthesis
Transcription
Translation

27. Protein Functions…. Metabolism (enzymes are proteins)
Structural (build form)
Transport (ex- hemoglobin)
Protection (antibodies are proteins)
Cell communication (hormones)

28. Review of Protein Structure…
Only 20 different common amino acids
Hundreds of thousands of different proteins !
Structure determines function !

29. 10.6 The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits
DNA specifies traits by dictating protein synthesis.
The molecular chain of command is from
DNA in the nucleus to RNA and
RNA in the cytoplasm to protein.
__________________ is the synthesis of RNA under the direction of DNA.
__________________ is the synthesis of proteins under the direction of RNA.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. Consider placing the basic content from Figure 10.6A on the board, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail.
Teaching Tips
1. It has been said that everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to evaluate the validity of this statement.
2. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
© 2012 Pearson Education, Inc. 29

30. Nucleotides: 2 types DNA & RNA
3 parts of RNA (the other nucleic acid) nucleotide
sugar = _________
phosphate group
nitrogenous base (A,U,C,G)
U=Uracil

31. 3 Types of RNA Required for Protein Synthesis
mRNA= messenger RNA
tRNA= transfer RNA
rRNA= ribosomal RNA
mRNA Assembled in nucleus
Single strand of RNA nucleotides
tRNA Found in the cytoplasm
Brings amino acid to the ribosome for polypeptide assembly
Single strand, folded back
2 important sections of strand
Anticodon
Amino acid binding end
rRNA Makes up the ribosome
Lines up mRNA for “reading”/transcription

32. DNA Transcription RNA NUCLEUS CYTOPLASM Translation Protein
Figure 10.6A_s3 The flow of genetic information in a eukaryotic cell (step 3)
Protein 32

33. T A C T T C A A A A T C A T G A A G T T T T A G A U G A A G U U U U A
Figure 10.8B_s3
Strand to be transcribed T A C T T C A A A A T C
DNA A T G A A G T T T T A G
Transcription
RNA A U G A A G U U U U A G
Figure 10.8B_s3 Deciphering the genetic information in DNA (step 3)
Start codon
Stop codon
Translation
Polypeptide
Met
Lys
Phe 33

34. 10.6 The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits
The connections between genes and proteins
The initial one gene–one enzyme hypothesis was based on studies of inherited metabolic diseases.
The one gene–one enzyme hypothesis was expanded to include all proteins.
Most recently, the one gene–one polypeptide hypothesis recognizes that some proteins are composed of multiple polypeptides.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. Consider placing the basic content from Figure 10.6A on the board, noting the sequence, products, and locations of transcription and translation in eukaryotic cells. This reminder can create a quick concept check for students as they learn additional detail.
Teaching Tips
1. It has been said that everything about an organism is an interaction between the genome and the environment. You might wish to challenge your students to evaluate the validity of this statement.
2. The information in DNA is used to direct the production of RNA, which in turn directs the production of proteins. However, in Chapter 3, four different types of biological molecules were noted as significant components of life. Students who think this through might wonder, and you could point out, that DNA does not directly control the production of carbohydrates and lipids. So how does DNA exert its influence over the synthesis of these two chemical groups? The answer is largely by way of enzymes, proteins with the ability to promote the production of carbohydrates and lipids.
© 2012 Pearson Education, Inc. 34

35. 10.9 Transcription produces genetic messages in the form of RNA
Overview of transcription
An RNA molecule is transcribed from a DNA template by a process that resembles the synthesis of a DNA strand during DNA replication.
RNA nucleotides are linked by the transcription enzyme RNA polymerase.
Specific sequences of nucleotides along the DNA mark where transcription begins and ends.
The “start transcribing” signal is a nucleotide sequence called a promoter.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. As students learn about transcription, they might wonder which of the two strands of DNA is read. This uncertainty may add to the confusion about the details of the process, and students might not even think to ask. As noted in Module 10.9, the location of the promoter, a specific binding site for RNA polymerase, determines which strand is read.
Teaching Tips
Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away.
© 2012 Pearson Education, Inc. 35

36. Direction of transcription Template strand of DNA
Free RNA nucleotides
RNA polymerase T C C A A T A U T C T G U G A C C A U C C A C A G T A G G T T A
Figure 10.9A A close-up view of transcription
Direction of transcription
Template strand of DNA
Newly made RNA 36

37. 10.9 Transcription produces genetic messages in the form of RNA
Transcription begins with initiation, as the RNA polymerase attaches to the promoter.
During the second phase, elongation, the RNA grows longer.
As the RNA peels away, the DNA strands rejoin.
Finally, in the third phase, termination, the RNA polymerase reaches a sequence of bases in the DNA template called a terminator, which signals the end of the gene.
The polymerase molecule now detaches from the RNA molecule and the gene.
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. As students learn about transcription, they might wonder which of the two strands of DNA is read. This uncertainty may add to the confusion about the details of the process, and students might not even think to ask. As noted in Module 10.9, the location of the promoter, a specific binding site for RNA polymerase, determines which strand is read.
Teaching Tips
Another advantage to the use of RNA to direct protein synthesis is that the original code (DNA) remains safely within the nucleus, away from the many potentially damaging chemicals in the cytoplasm. This is like making photocopies of important documents for study, keeping the originals safely stored away.
© 2012 Pearson Education, Inc. 37

38. Terminator DNA RNA polymerase DNA of gene Promoter DNA Initiation1
Initiation 2
Elongation
Area shown in Figure 10.9A
Figure 10.9B The transcription of a gene
Growing RNA 3
Termination
Completed RNA
RNA polymerase 38

39. 10.10 Post-Transcriptional Modification: Eukaryotic RNA is processed before leaving the nucleus as mRNA
Messenger RNA (mRNA)
encodes amino acid sequences and
conveys genetic messages from DNA to the translation machinery of the cell, which in
prokaryotes, occurs in the same place that mRNA is made, but in
eukaryotes, mRNA must exit the nucleus via nuclear pores to enter the cytoplasm.
Eukaryotic mRNA has
introns, interrupting sequences that separate
exons, the coding regions.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading.
© 2012 Pearson Education, Inc. 39

40. 10.10 Post-Transcriptional Modification: Eukaryotic RNA is processed before leaving the nucleus as mRNA
Eukaryotic mRNA
RNA splicing
Additions- cap and tail
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
Many analogies can be developed to represent the selective expression of a gene requiring the deletion of introns. Instructors that only assign some modules of a chapter are treating the chapters like sections of exons and introns, portions to be read and portions to be skipped. Alternately, students who highlight a chapter might be thought of as editing the book into exons, portions to be reviewed, and introns, nonhighlighted sections that will not be studied. Both analogies are imperfect, but may still convey the concept of selective reading. 40

41. Transcription Addition of cap and tail Cap
Exon
Intron
Exon
Intron
Exon
DNA
Transcription Addition of cap and tail
Cap
RNA transcript with cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
Figure The production of eukaryotic mRNA
NUCLEUS
CYTOPLASM 41

42. 10.11 Transfer RNA molecules serve as interpreters during translation
Transfer RNA (tRNA)
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
The unique structure of tRNA, with binding sites for an amino acid and its codon, permits the translation of the genetic code. Like an interpreter who speaks two languages, the tRNA molecules match codons to the specified amino acid.
© 2012 Pearson Education, Inc. 42

43. 10.12 Ribosomes build polypeptides
rRNA along with protein makes the ribosome.
Translation occurs on the surface of the ribosome
Student Misconceptions and Concerns
Ribosomes coordinate the functioning of mRNA and tRNA and, ultimately, the synthesis of polypeptides.
Ribosomes have two subunits: small and large.
Each subunit is composed of ribosomal RNAs and proteins.
Ribosomal subunits come together during translation.
Ribosomes have binding sites for mRNA and tRNAs.
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. Students might wonder why the details of transcription and translation are important. As the text notes, differences in the composition of prokaryotic and eukaryotic ribosomes form the basis of action for antibiotics. By identifying differences, we can develop drugs that target crucial features of prokaryotic pathogens without harming their eukaryotic hosts.
2. Ribosomal RNA is transcribed in the nucleolus of eukaryotic cells. The ribosomal subunits are assembled in the nucleus using proteins imported from the cytosol. These subunits are then exported to the cytosol, where they are only assembled into a functional ribosome when they attach to an mRNA molecule. Some of these details are not specifically noted in the text, but may be required to fill out your explanations.
3. If you use a train analogy for the assembly of monomers into polymers, the DNA and RNA trains are traded in on a three-for-one basis for the polypeptide train during translation. In general, this produces polypeptides that have about one-third as many monomers as the mRNA that coded for them.
© 2012 Pearson Education, Inc. 43

44. 10.7 Genetic information written in codons is translated into amino acid sequences
The sequence of nucleotides in DNA provides a code for constructing a protein.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. The transcription of DNA into RNA is like a reporter’s transcription of a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written language.
2. The sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame (see Module 10.16).
© 2012 Pearson Education, Inc. 44

45. 10.7 Genetic information written in codons is translated into amino acid sequences
The flow of information from gene to protein is based on a triplet code: the genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of nonoverlapping three-base “words” called codons.
Each amino acid is specified by a codon.
64 codons are possible.
Some amino acids have more than one possible codon.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. The transcription of DNA into RNA is like a reporter’s transcription of a political speech. In both situations, the language remains the same, although in the case of the reporter, it changes its form from spoken to written language.
2. The sequential information in DNA and RNA is analogous to the sequential information in the letters of a sentence. This analogy is also helpful when explaining the impact of insertion or deletion mutations that cause a shift in the reading frame (see Module 10.16). 45

46. 10.8 The genetic code dictates how codons are translated into amino acids
Characteristics of the genetic code
_______ nucleotides specify one amino acid.
61 codons correspond to amino acids.
AUG is the start codon; codes for methionine and signals the start of transcription.
3 “stop” codons signal the end of translation; _____, ____, ____
__________- with more than one codon for some amino acids
_______________- the genetic code is shared by organisms from the simplest bacteria to the most complex plants and animals
Student Misconceptions and Concerns
Three nucleotides specify one amino acid.
61 codons correspond to amino acids.
AUG codes for methionine and signals the start of transcription.
3 “stop” codons signal the end of translation.
Redundant, with more than one codon for some amino acids
nearly Universal—the genetic code is shared by organisms from the simplest bacteria to the most complex plants and animals
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. You may want to note the parallel between the discovery in 1799 of the Rosetta stone, which provided the key that enabled scholars to crack the previously indecipherable hieroglyphic code, and the cracking of the genetic code in Consider challenging your students to explain what part of the genetic code is similar to the Rosetta stone. This could be a short in-class activity for small groups.
2. The authors note the universal use of the genetic code in all forms of life. The evolutionary significance of this fundamental, universal language is a reminder of the shared ancestry of all life. The universal genetic code is part of the overwhelming evidence for evolution.
© 2012 Pearson Education, Inc. 46

47. GENETIC CODE

48. 10.13 An initiation codon marks the start of an mRNA message (Initiation)
Translation can be divided into the same three phases as transcription:
initiation,
elongation, and
termination.
Initiation brings together…
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. Ribosomal RNA is transcribed in the nucleolus of eukaryotic cells. The ribosomal subunits are assembled in the nucleus using proteins imported from the cytosol. These subunits are then exported to the cytosol, where they are only assembled into a functional ribosome when they attach to an mRNA molecule. Some of these details are not specifically noted in the text, but may be required to fill out your explanations.
2. If you use a train analogy for the assembly of monomers into polymers, the DNA and RNA trains are traded in on a three-for-one basis for the polypeptide train during translation. In general, this produces polypeptides that have about one-third as many monomers as the mRNA that coded for them. 48

49. 10.13 An initiation codon marks the start of an mRNA message (Initiation)
Initiation establishes where translation will begin.
Initiation occurs in two steps.
An mRNA molecule binds to a small ribosomal subunit and the first tRNA binds to mRNA at the start codon.
The start codon reads AUG and codes for methionine.
The first tRNA has the anticodon UAC.
A large ribosomal subunit joins the small subunit, allowing the ribosome to function.
The first tRNA occupies the P site, which will hold the growing peptide chain.
The A site is available to receive the next tRNA.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. Ribosomal RNA is transcribed in the nucleolus of eukaryotic cells. The ribosomal subunits are assembled in the nucleus using proteins imported from the cytosol. These subunits are then exported to the cytosol, where they are only assembled into a functional ribosome when they attach to an mRNA molecule. Some of these details are not specifically noted in the text, but may be required to fill out your explanations.
2. If you use a train analogy for the assembly of monomers into polymers, the DNA and RNA trains are traded in on a three-for-one basis for the polypeptide train during translation. In general, this produces polypeptides that have about one-third as many monomers as the mRNA that coded for them.
© 2012 Pearson Education, Inc. 49

50. 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation
Once initiation is complete, amino acids are added one by one to the first amino acid.
Elongation is the addition of amino acids to the polypeptide chain.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help students better remember details of translation, they might think of the letters for the two sites as meaning A for addition, where an amino acid is added, and P for polypeptide, where the growing polypeptide is located.
2. If you use a train analogy for the assembly of monomers into polymers, the DNA and RNA trains are traded in on a three-for-one basis for the polypeptide train during translation. In general, this produces polypeptides that have about one-third as many monomers as the mRNA that coded for them.
© 2012 Pearson Education, Inc. 50

51. 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation
Each cycle of elongation has three steps.
Codon recognition: The anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome.
Peptide bond formation: The new amino acid is joined to the chain.
Translocation: tRNA is released from the P site and the ribosome moves tRNA from the A site into the P site.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help students better remember details of translation, they might think of the letters for the two sites as meaning A for addition, where an amino acid is added, and P for polypeptide, where the growing polypeptide is located.
2. If you use a train analogy for the assembly of monomers into polymers, the DNA and RNA trains are traded in on a three-for-one basis for the polypeptide train during translation. In general, this produces polypeptides that have about one-third as many monomers as the mRNA that coded for them.
© 2012 Pearson Education, Inc. 51

52. Elongation Polypeptide Amino acid Anticodon mRNA Codons
P site
A site
Anticodon
mRNA
Codons 1
Codon recognition
mRNA movement
Stop codon
Figure 10.14_s4 Polypeptide elongation (step 4) 2
Peptide bond
formation
New peptide bond 3
Translocation 52

53. 10.14 Elongation adds amino acids to the polypeptide chain until a stop codon; termination
Termination stage of translation, when
the ribosome reaches a stop codon,
the completed polypeptide is freed from the last tRNA, and
the ribosome splits back into its separate subunits.
Student Misconceptions and Concerns
Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
Teaching Tips
1. Students might want to think of the A and P sites as stages in an assembly line. The A site is where a new amino acid is brought in, according to the blueprint of the codon on the mRNA. The P site is where the growing product/polypeptide is anchored as it is being built. To help students better remember details of translation, they might think of the letters for the two sites as meaning A for addition, where an amino acid is added, and P for polypeptide, where the growing polypeptide is located.
2. If you use a train analogy for the assembly of monomers into polymers, the DNA and RNA trains are traded in on a three-for-one basis for the polypeptide train during translation. In general, this produces polypeptides that have about one-third as many monomers as the mRNA that coded for them.
© 2012 Pearson Education, Inc. 53

54. Review: The flow of Genetic information in the cell is DNA RNA Protein
Transcription
DNA
mRNA 1
Transcription
RNA polymerase
Translation
CYTOPLASM 2
Amino acid
Amino acid
attachment
Enzyme
tRNA
ATP
Anticodon
Initiator tRNA
Large ribosomal subunit 3
Initiation of
polypeptide synthesis
Start Codon
Small ribosomal subunit
mRNA
New peptide bond forming
Growing polypeptide
Figure A summary of transcription and translation 4
Elongation
Codons
mRNA
Polypeptide 5
Termination
Stop codon 54

55. 10.16 Mutations can change the meaning of genes
A mutation is any change in the nucleotide sequence of DNA.
Mutations can involve
large chromosomal regions or
just a single nucleotide pair.
Mutations can be spontaneous (mistakes during replication) or caused by mutagens.
Examples- UV light, chemicals
Student Misconceptions and Concerns
1. Beginning college students are often intensely focused on writing detailed notes. The risk is that they will miss the overall patterns and the broader significance of the topics discussed. Consider a gradual approach to the subjects of transcription and translation, beginning quite generally and testing comprehension, before venturing into the finer mechanics of each process.
2. Mutations are often discussed as part of evolutionary mechanisms. In this sense, mutations may be considered a part of a creative process. The dual nature of mutations, potentially deadly yet potentially innovative, should be clarified.
Teaching Tips
1. A simple way to demonstrate the effect of a reading frame shift is to have students compare the following three sentences. The first is a simple sentence. However, look what happens when a letter is added (2) or deleted (3). The reading frame, or words, are re-formed into nonsense.
(1) The big red pig ate the red rag.
(2) The big res dpi gat eth ere dra g.
(3) The big rep iga tet her edr ag.
2. The authors have noted elsewhere that “A random mutation is like a random shot in the dark. It is not likely to improve a genome any more than shooting a bullet through the hood of a car is likely to improve engine performance!”
© 2012 Pearson Education, Inc. 55

56. 10.16 Mutations can change the meaning of genes
. A mutation can be:
Harmful, giving rise to cancers.
Cause genetic disorders (if in sperm or egg)
Create new traits/variation
in the species

57. Sickle-cell hemoglobin
Figure 10.16A
Normal hemoglobin DNA
Mutant hemoglobin DNA C T T C A T
mRNA
mRNA G A A G U A
Normal hemoglobin
Figure 10.16A The molecular basis of sickle-cell disease
Sickle-cell hemoglobin
Glu
Val 57

58. Nucleotide substitution
Figure 10.16B
Normal gene A U G A A G U U U G G C G C A
mRNA Protein
Met
Lys
Phe
Gly
Ala
Nucleotide substitution A U G A A G U U U A G C G C A
Met
Lys
Phe
Ser
Ala U
Deleted
Nucleotide deletion A U G A A G U U G G C G C A U
Figure 10.16B Types of mutations and their effects
Met
Lys
Leu
Ala
His
Inserted
Nucleotide insertion A U G A A G U U G U G G C G C
Met
Lys
Leu
Ala
His 58

59. You should now be able to
Compare the structures of DNA and RNA.
State the contributions of Chargaff, Franklin, Wilkins, Watson and Crick to our understanding of DNA.
Describe the process of DNA replication. State the role of helicase, DNA polymerases, primase, and DNA ligase
Describe the general purpose of protein synthesis; relate DNA sequence to the specific protein produced. 59

60. You should now be able to
State the general flow of genetic information as genes are expressed.
Explain transcription and how mRNA is produced using DNA.
Explain how eukaryotic RNA is processed before leaving the nucleus.
Discuss the role of mRNA, tRNA and rRNA in translation.
Explain translation; initiation, elongation, translocation and termination. 60

61. You should now be able to
Describe the structure and function of ribosomes
.Define mutation, causes of mutations, and potential consequences.
State the amino acid sequence in a polypeptide given the mRNA.
© 2012 Pearson Education, Inc. 61

62. Practice DNA is TACAGGCGATGGATT mRNA is ____________________
Divide into codons (reading frames)
Amino acids coded for are:

63. Helpful sites
(there are selections at this site that will help with replication, transcription and translation)

64. is a polymer made from monomers called DNA (a)
Figure 10.UN03
is a polymer made from monomers called
DNA
(a)
is performed by an enzyme called
(b)
(c)
(d)
comes in three kinds called
RNA
(e)
(f)
molecules are components of
Figure 10.UN03 Connecting the Concepts, question 1
use amino-acid-bearing molecules called
(g)
is performed by structures called
(h)
one or more polymers made from monomers called
Protein
(i) 64

65. STRUCTURE OF DNA Double Helix A=T and C=G A-T and C-G
Two sugar – phosphate backbones
Four kinds of nucleotides
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
A=T and C=G
Purine pairs with a pyrimidine
A-T and C-G
Purines (2 rings)
Pyrimidines (1 ring)

66. DNA Replication SEMICONSERVATIVE 1. Helix unwinds
2. 2 strands separate
3. Free nucleotides bind to open bases according to pairing rules
(parent strand acts as template)
4. 2 identical strands consist of one parent strand and one newly formed strand.

67. ANIMATION…Replication

68. Transcription- overview
Transcribing (writing) information from DNA
Takes place in the nucleus
Promoter region is recognized by RNA polymerase as a start location
Assembles mRNA strand
mRNA

69. Post Transcriptional Modifications
In eukaryotic cells, mRNA is modified before leaving nucleus
Introns are removed
Exons are spliced together
“Cap” is added to beginning of strand
“poly-A tail” (many adenine ribonucleotides) are added to end
Different types of slicing may occur for a single transcript; one gene can specify 2 or more slightly different proteins!