eukaryotic genome regulation-genes not...

AP Bio 2013/14 Nickel OKM

Unit 3 – Genetic Information

Brilliant Biologist: ____________________________

Deadline: ____________________________________________

To Do Checklist:

1. Reading Guides: Chapter 16,17,18,19 (page 2-27) ______

2. Bozeman Biology Videos (page 28) ______

3. What you should know! (pg 29-45)

3. Prezis ______

AP Bio- Molecular Genetics 1: DNA Introduction on PreziAP Bio- Molecular Genetics 2: The Central Dogma on PreziAP Bio- Molecular Genetics 3: Regulation of Gene Expression on PreziAP Bio- Molecular Genetics 4: Viruses on PreziAP Bio- Molecular Genetics 5- Biotechnology on Prezi

4. Labs/Activities ______a) DNA Model Challenge (pg 46)b) DNA paper model – teacher will providec) Working with Code (pg 47-48) d) DNA analogy (pg 49) b) Fun with Translation – teacher will providec) Know your molecules (pg 50 – 51)

5. Vocab (page 52-55) ______

7. Student Objectives (page 56-62) ______

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http://prezi.com/

http://prezi.com/-rsuasafhata/ap-bio-molecular-genetics-5-biotechnology/

http://prezi.com/

http://prezi.com/bdrtbhglgy4c/ap-bio-molecular-genetics-4-viruses/

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http://prezi.com/jgpqmkmh7xk5/ap-bio-molecular-genetics-3-regulation-of-gene-expression/

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http://prezi.com/rjwxngctmqlp/ap-bio-molecular-genetics-2-the-central-dogma/

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http://prezi.com/zkhjbh03vcri/ap-bio-molecular-genetics-1-dna-introduction/


Chapter 16 Guided Reading Assignment

1. Explain Griffith’s experiment and the concept of transformation in detail.

2. What did Avery, MacLeod and McCarty contribute to this line of investigation?

3. What is a bacteriophage?

4. Label the diagram below and explain the Hershey Chase experiment.

5. How did Chargraff’s work contribute to understanding the structure of DNA?

6. Why was Rosalind’s Franklin’s work essential to the understanding of the structure of DNA?

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7. Label the structure below:

8. Why does adenine always pair with thymine and guanine with cytosine in DNA?

9. What is meant by the term that DNA replication is semiconservative?

10. Detail the Meselson and Stahl experiment concerning DNA replication.

11. How is bacterial DNA replication accomplished?

12. What are DNA polymerases?

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13. In your own words, what is meant by the term – DNA is antiparallel in arrangement”?

14. Define the following terms:a. Leading strand

b. Lagging strand

c. Okazaki fragments

d. DNA ligase

e. Primer

15. Label the diagram below:

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16. Identify and label the diagram below:

17. List the functions of the following enzymes:a. Helicase

b. Single stranded binding protein

c. Topoisomerase

d. Primase

e. DNA Polymerase III

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f. DNA Polymerase I

g. DNA Ligase

18. Identify and label the diagram below:

19. What is mismatch repair?

20. Label the diagram below:

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21. Why is there a short section of a cell’s DNA that cannot be repaired or replaced? Draw your own diagram explaining the problem. It is very important that you understand this conceptually.

22. What are telomeres and why are they important? How does telomerase play a role?

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1. What did Garrod mean by “inborn errors of metabolism?”

2. Describe the Beadle and Tatum experiment with mold in detail – use the diagram below to help. The logic behind both the experiment and the results are critical.

3. What was Beadle and Tatum’s final hypothesis?

4. Use the diagram below to note the flow of genetic information in a eukaryotic cell – next to each label in the square – write the definition of the term.

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5. Why does the “code” have to be in triplets and not singles or doubles?

6. What is the template strand?

7. Compare and contrast the codon and anticodon?

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8. How did Nirenberg “figure out” which amino acids went with which codes?

9. What is the reading frame?

10. What conclusions can be drawn from the similarities of the genetic code among living organisms?

11. Use the diagram below to understand transcription: Define all terms.

12. What is a transcription unit?

13. Describe the prokaryotic promoter and terminator.

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14. Use the diagram below to demonstrate initiation of transcription at a eukaryotic promoter. Write definition of all terms in diagram.

15. Contrast termination of transcription for prokaryotic and eukaryotic organisms.

16. Why is important that the promoter be upstream of the transcription unit?

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17. Why is RNA processing necessary?

18. What does adding a 5’ cap and poly A tail mean and why is it important?

19. Define the following terms:a. RNA splicing

b. Introns

c. Exons

d. Spliceosome

e. snRNP’s

f. ribozymes

g. UTR

h. Alternative RNA splicing

i. domains

20. Describe the structure and function of transfer RNA.

21. Why is the enzyme aminoacyl-tRNA synthetase important to translation and protein synthesis?

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22. What is “wobble”?

23. Describe the structure and function on ribosomal RNA – use the diagram below.

24. Detail the steps of initiation of translation.

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25. Use the diagram below to detail elongation cycle of translation. Define terms.

26. Use the diagram below to detail the termination of translation – define all terms.

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27. What are polyribosomes?

28. What is an example of a post translational modification of a protein?

29. What is a signal peptide?

30. What is a signal recognition particle?

31. Use the diagram below to highlight the signal mechanism for targeting proteins to the ER.

32. You are responsible for the content in Table 17.1 on page 327.

33. Define the following terms:a. Mutations

b. Point mutations

c. Base pair substitution

d. Missense

e. Nonsense

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f. Insertions

g. Deletions

h. Frameshift mutation

i. Mutagen

34. How has a gene been “redefined” and why?

35. Use the diagram below to help you study the “whole” picture.

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1. How and what did Dr. Mayer discover specifically in 1883?

2. What did Ivanowsky conclude that built on Mayer’s work?

3. What logic did Beijerinck use to lead to the idea of a virus?

4. How was the existence of a virus finally confirmed and by whom?

5. How small are viruses?

6. What kind of nucleic acids are the viral genomes made of?

7. What is the name for a protein shell enclosing the viral genome?

8. What are the subunits of capsids?

9. What are viral envelopes and what is their function?

10. Where are the most complex capsids found?

11. Define host range.

12. List the full steps of the simplified viral reproductive cycle.

13. What is the phage reproductive cycle that culminates in the death of the host cell?

14. What kind of phage only reproduces by a lytic cycle?

15. How do bacteria defend themselves against phages?

16. What are the steps of the lytic cycle of a T4 phage?

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17. What is the phage reproductive cycle that replicates the phage genome without destroying the host?

18. What are phages called that care capable of using both modes of reproduction?

19. What is a prophage?

20. What is an example of the interaction between a prophage and a bacterium?

21. What is the use of a viral envelope in animal viruses?

22. Does this reproductive cycle kill the host cell?

23. What are retroviruses and how do they use reverse transcriptase?

24. Describe the reproductive cycle of an enveloped RNA virus.

25. Describe the reproductive cycle of HIV, a retrovirus.

26. Is it believed that viruses evolved before or after the first cells appeared and what evidence is used to support the idea?

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27. What are vaccines?

28. What are the three processes that contribute to the emergence of viral diseases?

29. List and explain the two major routes that plant viruses are spread.

30. What are viroids?

31. Define prions.

32. What is the main component of most bacterial genomes?

33. How is the DNA arranged in the nucleoid region of the bacterial genome?

34. What is a plasmid?

35. Describe the process of binary fission.

36. Why do mutations make such a large contribution to bacterial genetic variation as compared to humans?

37. Explain the experiment and the results that demonstrated evidence of genetic recombination in bacteria.

38. What is the process of alteration of a bacterial cell’s genotype by the uptake of naked, foreign DNA from the surrounding environment?

39. What famous experiment in the previous unit described this process?

40. Define transduction.

41. List the generalized steps of transduction.

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42. What is the process of direct transfer of genetic material between two bacterial cells that are temporarily joined?

43. What structure joins them?

44. What generally must be present for the sex pili to donate DNA during conjugation?

45. What is special about the F plasmid?

46. What is an episome?

47. What are R plasmids and why are these a problem to humans?

48. How does this relate to natural selection?

49. Define transposable elements.

50. Do transposable elements exist independently?

51. What is a common name for transposable elements?

52. What is the name for the simplest transposable elements?

53. What is the name for transposable elements that are longer and more complex than insertion sequences?

54. What is an example of the benefit to bacteria of these transposable elements?

55. What are the two ways that metabolic control can occur within bacteria?

56. What is the key advantage of grouping genes of related function in to one transcription unit?

57. What is this “switch” called?

58. Where is an operator positioned?

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59. What does the operator control?

60. What is the name for the operator, promoter, and the genes they control?

61. What can happen if the trp operan is turned “on”?

62. What turns the “switch” off?

63. How does a repressor work?

64. What gene controls the making of the trp repressor protein?

65. What are the two states that the operator vacillates (switches between)?

66. How is the trp repressor protein and allosteric protein?

67. Define corepressor.

68. What are the two methods of negative gene regulation?

69. Why is the trp operan considered repressible?

70. What is the definition of an inducible operan?

71. What does the inducer do?

72. Why are repressible enzymes generally associated with anabolic pathways and how is this an advantage to the organism?

73. How does positive gene regulation work?

74. We stated in the beginning of the year that negative feedback has an on/off switch and positive feedback can only amplify the response – how does this statement connect with negative and positive gene regulation?

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1. Define the following terms:a. Chromatin

b. Nucleosome

2. Outline the levels of DNA packing in the eukaryotic nucleus below next to the diagram provided.

3. What is the difference between heterochromatin and euchromatin? Which is transcribed?

4. What is cell differentiation?

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5. IF cells carry all of the genetic differences, why then are cells so unique – what is responsible for this?

6. In the diagram below – highlight all of the potential locations for gene expression regulation in eukaryotic cells. How does this compare with prokaryotic cells?

7. What effect do the following have on gene expression?a. Histone acetylation

b. Histone deacteylation

c. DNA methylation

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8. How does methylation relate to genomic imprinting?

9. Define epigenetic inheritance.

10. How do the following control elements assist in regulation?a. Transcription factors

b. Enhancers

c. Activators

d. Repressors

11. Use the diagram below to explain the interactions of enhancers and transcription activators.

12. Explain how RNA processing is a mechanism of post-transcriptional regulation.

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13. What role do microRNA’s play in post-transcriptional regulation? Use the diagram below to help you explain.

14. What is RNA interference?

15. How does translation provide another opportunity for control?

16. What is a proteasomes?

17. What is the difference between oncogenes,proto-oncogenes and tumor-suppressor genes?

18. What is the ras gene?

19. What is the p53 gene?

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20. Label the diagram below that describes the signaling pathways that regulate cell division.

21. Why is said that people inherit predispositions to cancer not cancer itself?

22. What are the types of DNA sequences in the human genome and what % of the genome are they?

23. What is the difference between transposons and retrotransposons. Use the diagram below to help you answer the question.

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24. What are Alu elements?

25. What are multi-gene families?

26. What are pseudogenes?

27. How can errors during meiosis lead to duplication of genes?

28. What are three ways transposable elements are thought to have contributes to the evolution of the genome?

.Bozeman Biology Videos

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Chapter 16

Meselson Stahl ExperimentDNA Structure DNA Replication

Chapter 17

Transcription & Translation Regulation and Timing in Development (AP Essentials #24)DNA & RNA Part I (history) (Biology Essentials #27 A)DNA & RNA Part II (structure) (Biology Essentials #27 B)Central Dogma: TranscriptionThe Beadle-Tatum Experiment

Chapter 18

Gene Regulation (AP Essentials #31)Signal Transmission and Gene Expression (AP Essentials #32)Regulation and Timing in Development(AP Essentials #24)

Chapter 19

Viral Replication (AP Essentials #35

Viruses

Biotechnology: Molecular Biology

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CHAPTER 16: DNA, RNA, PROTEINSNUCLEIC ACIDS (DNA & RNA) = “Information” molecules

CHARGAFF’S RULES: A = T and G = CA Purine always bonds to a Pyrimidine

RIBONUCLEIC ACID (RNA)• Single stranded• Sugar = ribose• Nitrogenous bases = A, U, G, C (NO T)• Can fold up in 3D shape

DEOXYRIBONUCLEIC ACID (DNA)• Double stranded• Sugar = deoxyribose• Nitrogenous bases = A, T, G, C (NO U)• Strands run in opposite directions (ANTIPARALLEL) • Ladder twists into a DOUBLE HELIX• Backbone = sugars and phosphates• Rungs of ladder = nitrogenous bases• Hydrogen bonds between nitrogenous bases hold sides of ladder together

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NUCLEOTIDE SUBUNITSSUGAR = Ribose (RNA) OR Deoxyribose (DNA)NITROGEN BASES:

DNA RNAAdenine

Adenine

Guanine

Guanine

Cytosine

Cytosine

Thymine

Uracil


EVOLUTION: Structural/functional evidence supports the relatedness of all domains • Genetic code is shared by all modern living systems• Linear chromosomes in eukaryotes show relatedness

REPLICATION (DNA → DNA) Site where it starts = ORIGIN of REPLICATION Place where nucleotides add = REPLICATION FORK Prokaryote- single starting spot Eukaryotes-multiple sites

DNA POLYMERASE • reads code strand in 3’ → 5’ direction • builds a new strand in 5’→3’ direction • adds on to 3’ end of sugar in previous nucleotide

Splitting phosphates from nucleotide triphosphate subunits provides energy for reaction

DNA POLYMERASE CAN’T START A CHAIN by itself; • can only add nucleotides to 3’ end of an existing DNA/RNA chain• needs RNA primer to start chain • evidence for RNA as first info molecule (RNA World Theory) HELICASE- untwists double helix to open strands at replication forks TOPOISOMERASE- relieves strain caused by untwisting SINGLE-STRAND BINDING PROTEINS-

stabilize unpaired strands to hold them open PRIMASE-starts segment by adding RNA primer sequence DNA POLYMERASE I –

removes RNA primers and replaces them with DNA bases by adding to the 3’ end of the previous fragment

LIGASE-joins Okazaki fragments together to make a continuous copied strand

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LEADING STRAND (runs 3’→ 5’) copies toward the replication forkPRIMASE adds RNA primer to start chain DNA POLYMERASE III adds nucleotides in 5’ → 3’ direction LAGGING STRAND (runs 5’→ 3’) copies away from replication forkPRIMASE adds RNA primers at various spots as


IMPORTANT: Because DNA polymerase can’t fill in last section when primer is removed from lagging strand, the code shortens with each replication

TELOMERE sequences at ends of chromosomesprevent erosion of essential information in code with each replicationTELOMERASE = enzyme that lengthens telomeres • found in eukaryotic germ cells that divide frequently

to produce gametes• may play a role in a aging and cancer

PROOFREADING & REPAIR

Mistakes in final DNA: 1 in 10 billionMistakes in initial base pairing during replication 1 in 100,000DNA POLYMERASE proofreads each base as it’s added & fixes errorsErrors can come from “proofreading mistakes” that are not caught OR environmental damage (Ex: X-rays, UV light, chemical mutagens/carcinogens)

NUCLEOTIDE EXCISION-REPAIR • Cells continually monitor DNA and make repairs • NUCLEASES- DNA cutting enzymes remove errors• DNA POLYMERASE fills in gap using complimentary strand• LIGASE seals ends

Ex: THYMINE DIMERS = joins THYMINES in same strand• damage caused by UV light • can be repaired

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LEADING STRAND (runs 3’→ 5’) copies toward the replication forkPRIMASE adds RNA primer to start chain DNA POLYMERASE III adds nucleotides in 5’ → 3’ direction LAGGING STRAND (runs 5’→ 3’) copies away from replication forkPRIMASE adds RNA primers at various spots as


Xeroderma pigmentosum - genetic disorder can’t go out in sun mutation in DNA enzymes that repair UV increased skin cancer/cataracts

CHAPTER 17- FROM GENE TO PROTEIN

Central Dogma of Molecular Biology(Flow of information in cells)DNA → RNA → PROTEINS • GENE = sequence of DNA with a specific function (final product = polypeptide OR RNA) • RNA's = intermediates between DNA code and proteins that determine phenotype• For each gene only one of the two strands is transcribed into an RNA (template strand)• For some genes one strand may be used; for other genes the complementary strand is used

3 KINDS OF RNA involved in Protein synthesis Messenger RNA (mRNA) Transfer RNA (tRNA) Ribosomal RNA (rRNA)

MESSENGER RNA carries DNA message from nucleus to cytoplasm;

message is read in “triplets” called CODONS 64 different codons code for 20 different amino acids;

AUG = START codon; UAA, UAG, UGA are STOP codons; REDUNDANCY OR ”WOBBLE” - codons for same amino acid can differ in 3rd base Code = universal to all life (found in all organisms) = evidence for common ancestry Prokaryotes~ m-RNA functional as soon as transcribed Eukaryotes~ m-RNA must be processed before use GTP "cap" = METHYLATED GUANINE added to 5’ end; for stability; prevents degradation used to bind mRNA to ribosome PolyA "tail" added to 3’ end (AAA)- stability; helps passage through nuclear membrane

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DNA → DNA = REPLICATIONDNA → RNA= TRANSCRIPTIONRNA → PROTEINS = TRANSLATION


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In EUKARYOTES mRNA is made as pre-mRNA containing: • INTRONS- noncoding DNA segments may provide cross over places without interrupting code may facilitate evolution of new proteins by exon shuffling • EXONS - coding DNA segments; code for different DOMAINS =structural/functional regions

snRNPs (small nuclear ribonucleoproteins) • Made of proteins and RNA • Part of SPLICEOSOME (complex that edits pre-mRNA cuts out the introns and reattaches the remaining mRNA

ALTERNATIVE RNA SPLICING- can produce different proteins by editing mRNA in different ways EX: Immunoglobulins (antibodies) that match new antigens

RIBOZYMES = RNA molecules that function as enzymes EX: Some preRNA’s can self edit own introns;

TRANSFER RNA (tRNA) • cloverleaf-like secondary structure folds into L shape• brings amino acids to ribosome • attaches amino acids in proper place• ANTICODON region matches codon on mRNA

AMINOACYL-tRNA SYNTHETASE enzymeattaches a specific amino acid using energy from ATP

RIBOSOMES (=RYBOZYMES RNA that functions as an enzyme) Made up of rRNA (2/3) and PROTEINS (1/3) ; rRNA made in NUCLEOLUS in eukaryotes and assembled with proteins imported from

cytoplasm Large and small subuits join to form functional ribosome only when attach to mRNA; Ribosomes not making proteins exist as separate subunits Ribosomes making proteins for membranes/export: proteins are “tagged” so can be

attached to rough ER; Cytoplasmic proteins made on “free” ribosomes Prokaryotic and eukaryotic subunits are different sizes = evidence for Endosymbiotic

theory (PROKARYOTIC RIBOSOMES: 30S + 50S = 70S; EUKARYOTIC RIBOSOMES: 40S + 60S = 80S)

Subunit size is medically significant ~ Certain antibiotics work by inhibiting prokaryotic ribosomes without affecting

ribosomes of the eukaryotic host cell

RIBOSOME BINDS mRNA

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Has 3 tRNA BINDING SITES:A (AMINOACYL-tRNA site)- tRNA with new amino acid attaches P (PEPTIDYL-tRNA site) – peptide bond forms holds tRNA carrying growing polyeptide chain;

E (EXIT site) - empty tRNA exits

TRANSCRIPTION = DNA → RNA (Occurs in the NUCLEUS)

1. INITIATION RNA POLYMERASE binds to DNA at region called PROMOTER

LIKE DNA POLYMERASE: can only attach nucleotides in 5’ → 3’ direction; UNLIKE DNA POLYMERASE: can start a chain from scratch; no primer needed

In eukaryotes: TRANSCRIPTION FACTORS & TATA BOXES help position/bind to correct spot

RNA POLYMERASE separates the DNA strands to begin transcription2. ELONGATION

RNA chain grows in the 5' → 3' direction’ nucleotides base pair with template strand; nucleotides added to the 3’ end of preceding nucleotide (60 nucleotides/sec)

the non-coding strand of DNA reforms a DNA double helix by pairing with the coding strand

3. TERMINATION transcription proceeds until RNA polymerases reaches a TERMINATOR site on

the DNA; RNA molecule is then released Segment of DNA transcribed into one RNA = TRANSCRIPTION UNIT

* * * * * * * * * * * * ** *

TRANSLATION = RNA → PROTEINS (Occurs on RIBOSOMES in CYTOPLASM) Specific AMINO ACYL tRNA SYNTHETASES added amino acids to correct tRNA’s1. INITIATION

Small ribosomal subunit attaches to the 5' end of the mRNA ('start' codon - AUG)

energy comes from GTP (guanosine triphosphate) tRNA carries 1st amino acid (METHIONINE) to the

mRNA large ribosomal subunit attaches to the mRNA

2. ELONGATION Ribosome moves along mRNA matching tRNA

ANTICODONS with mRNA CODONS

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tRNA with new amino acid attaches at A site tRNA at A site moves to P site and receives growing chain tRNA a P site moves to E site and exits Released tRNA can recycle and bring in a new amino acid a new tRNA enters the A site and repeats the process increasing the polypeptide

chain length3. TERMINATION

occurs when the ribosome encounters a 'stop' codon ribosome subunits detach; polypeptide is released mRNA can be reread multiple time POLYSOMES- = strings of ribosomes

can work on same mRNA at same time

SIGNAL-RECOGNITION PARTICLE (SRP)Protein synthesis begins on free ribosomes Polypeptides that will become MEMBRANE PROTEINS or be SECRETED are markedSRP (SIGNAL RECOGNITION PARTICLE) attaches to protein signal sequence and receptor on ERGrowing protein chain is inserted into ER lumenComplex disconnects

POST TRANSLATIONAL MODIFICATION - Changes to polypeptide chain to make it a protein

CHAPARONINS-help wrap into 3D shape Some have groups added (sugars, lipids, phosphates, etc)

EX: glycoproteins (protein + sugar) Some have segments removed

EX: insulin made as one chain middle removed to become active

MUTATIONS• Not all harmful- can PROVIDE GENETIC VARIABILITY ~Foundation for NATURAL SELECTIONCan be: • Spontaneous (errors in replication, repair, recombination) • Caused by MUTAGENS EX: radiation, chemicals, cigarette smoke, etc = CARCINOGENS (can cause cancer)HARMFUL MUTATIONS- change protein function • POINT mutation: change in one base pair of a gene

Substitution- replace one base with another

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• SILENT- change codes for same amino acid (due to redundancy)

• MISSENSE-codes for another amino acid Changes protein sequence and usually function

Ex: sickle cell disease- T → A in hemoglobin • NONSENSE-code changes to STOP codon makes NONFUNCTIONAL protein

FRAMESHIFT • All nucleotides downstream are grouped incorrectly; • INSERTION/DELETION-causes FRAMESHIFT if not a multiple of 3• Causes more damage at beginning of gene than at end EX: O blood type allele is deletion in A blood type code

GENE REGULATION CHAPTERS 18 & 19 -Timing/coordination of specific events = necessary for normal development of organisms- cell differentiation results from the expression of genes for tissue- specific proteins- induction of transcription factors results in sequential gene expression. during development- Homeotic (HOX) genes are involved in developmental patterns and sequences - Embryonic induction in development results in the correct timing of events-. APOPTOSIS (programmed cell death ) plays a role in the development/differentiation- MICRO RNA’s- regulate genes/play role in development/ control of cellular functions - Genetic mutations can result in abnormal development- Environmental factors can influence gene expression EX: temperature and the availability of water determine seed germination in most plants.

PROKARYOTIC GENOME• use substances/synthesize macromolecules just fast enough to meet needs• If substance/enzyme needed, gene is transcribed. • If substance/enzyme not needed, gene is turned off• Allows for conservation of cell resources • Controlling gene expression is one method of regulating metabolism

OPERON – Related genes grouped together with one promoter• Allows for coordinated control of genes required for metabolism. • One switch controls more than one gene• Can be inducible or repressible. • Not present in eukaryotes Repressible and inducible enzymes = both examples of NEGATIVE control of a pathwayActivating the repressor proteins shuts off the pathway POSITIVE control requires that an activator molecule switch on transcription

OPERATORS- regions of DNA that control RNA access to promoterREPRESSOR - -regulatory protein binds to operator - turns genes off (negative control mechanism) - acts as a braking mechanism - produced at a site away from the operon by regulatory gene.

Repressors alternate between active/inactive forms to control transcription.• Active form- binds to operator/turns gene off• Inactive form- conformation change prevents binding to operator

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• Binding of REPRESSOR to OPERATOR prevents transcription -RNA polymerase not able to bind to promoter ~ TURNS GENE OFF -

Repressible Operons EX: trp operon Inducible Operons EX: lac operonTheir genes are switched on until a specific metabolite activates the repressor.

Their genes are switched off until a specific metabolite inactivates the repressor.

They generally function in ANABOLIC pathways. Function in CATABOLIC pathwaysPathway end product switches off its own production by repressing enzyme synthesis.

Enzyme synthesis is switched on bythe nutrient the pathway uses

REPRESSIBLE: TRYPTOPHAN trp OPERON Genes usually TURNED ON; Repressor = INACTIVE; Can be turned off by activating repressorAllows cell to use genes when tryptophan is needed and turn off genes when trp is plentiful

TRYPTOPHAN = corepressorPresence of tryptophan activates repressor

If TRYPTOPHAN is present, don’t need to make more

* * * * * * * * * * * * ** *

INDUCIBLE LACTOSE lac OPERON

Genes usually TURNED OFF; Repressor = ACTIVE; binds OPERATOR Can be turned ON by deactivating repressorAllows cell to turn on genes needed for lactose digestion when lactose is available

Keeps genes turned off unless needed

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ALLOLACTOSE =inducerpresence inactivates repressor

Cell only turns gene on when needed

EUKARYOTIC GENOME REGULATION-genes NOT grouped into operonsCHROMOSOME STRUCTUREDNA PACKING/CHEMICAL MODIFICATIONHISTONES wrap DNA into beadlike bundles = NUCLEOSOMESTight wrapping around HISTONES turns genes offAddition of ACETYL GROUPS to histones loosens wrapping HETEROCHROMATIN-tightly packedEUCHROMATIN-less tightly packedDNA METHYLATION-adding (–CH3) to cytosine blocks transcription EX: Barr bodies, genomic imprinting (epigenetics)

TRANSCRIPTIONAL CONTROLPROMOTER region at beginning of genebinding of RNA polymerase/transcripton factorscontrols speed of transcription

TATA BOX-helps position RNA Polymerase

ENHANCER sequences-upstream from genebinding of proteins here speeds up transcription POST TRANSCRIPTIONAL CONTROLRNA PROCESSING - Intron/exon editing - Alternative RNA splicing - 5’ CAP & Poly-A tail

NUCLEAR TRANSPORT -Control speed of exit out of nucleus

TRANSLATIONAL CONTROLRegulatory proteins prevent ribosome binding to 5’ end of mRNA Change rate of mRNA digestionChange rate of aminoacyl-tRNA synthetase recharging tRNA’s

POST-TRANSLATIONAL CONTROLRNAinterference (RNAi) – short RNA’s bind mRNA MICRO RNA (miRNA) - block reading of message by ribosomes SMALL INTERFERING (siRNA) RNA’s tag message for degradationCLEAVAGE-Cutting polypeptide chain to produce functional protein

EX: proinsulin (1 chain) → insulin (2 chains)CHEMICAL MODIFICATION- Add sugars, phosphates, etcTRANSPORT TAGS- Identify cellular destinationUBIQUITIN=protein tag identifies proteins for degradation digested by PROTEASOMES

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CHAPTER 18 VIRUSES Alive?Made of NUCLEIC ACID surrounded by PROTEIN COATTiny: smaller than ribosomesCan be double/single strandedCan have DNA/RNAProtein shell = CAPSIDSome have ENVELOPES around capsid that aid in host infectionBACTERIOPHAGES-viruses that infect bacteria Have no cellular machinery of their own Can only reproduce in host cells

RETROVIRUSES EX: HIV (AIDS virus) Have RNA for genetic code Contain REVERSE TRANSCRIPTASE enzyme ~ uses viral RNA to make a complementary DNA used by host cell Enzyme used as a genetic tool to turn eukaryotic mRNA into DNA that can be incorporated and transcribed by bacteria

TWO KINDS OF LIFE CYCLES

PRIONS = Misshaped infectious proteinsCause misfolding in proteins they contactAffect brain; untreatable and fatal

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LYTIC – ends in death of host cellvirus injects DNA into host cellTakes over cell’s machinery to make copies of viral DNA/proteinsVirus is assembledCell is lysed releasing multiple copies of virus

LYSOGENIC- Viral DNA incorporated into host DNAReplicates along with host DNAIncorporated viral DNA = PROPHAGECan stay in host DNA for yearsCertain conditions can cause prophage to leave host DNA and enter lytic cycle


EX: SCRAPIE in sheep; BOVINE SPONGIFORM ENCEPHALOPATHY (BSE) or “MAD COW DISEASE” in cows; CREUTZFELD-JAKOB and KURU in humans

PLASMIDS= Small circular self replicating DNA•separate from main bacterial chromosome•Carry 2-30 genes •Often carry genes for antibiotic resistance (R plasmids) •Can carry fertility genes (F factor) (See Conjugation below)

•Plasmids used as a genetic tool•Can be cut with RESTRICTION ENZYMES and used to incorporate foreign DNA into bacteria•Bacteria then reproduce, copying the inserted gene along with their own plasmidMECHANISMS OF GENE TRANSFER/GENETIC RECOMBINTION IN BACTERIA

20- DNA TECHNOLOGY

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TRANSFORMATIONUptake of naked DNA from another DNA sourceRemember . . .Griffith’s pneumonia/mice experiment

TRANSDUCTIONPhage viruses can pick up & transfer DNA to new host along with viral DNA

CONJUGATION = bacterial “sex” Bacteria with F factor plasmids can form sex pili Structure to directly transfer DNA to another bacteria


GENETIC ENGINEERING:manipulating genes and genomes

RECOMBINANT DNA . Combining DNA from different organisms

APPLICATIONS OF DNA TECHNOLOGY• DIAGNOSIS OF DISEASE Virus detection; ID genetic carriers/disorders• GENE THERAPY ID mutant genes; purify replacements• PHARMACEUTICAL PRODUCTION Bacterial production of insulin, Human Growth hormone• FORENSICS/PATERNITY Crime scene analysis Who’s the daddy?

• GENETICALLY MODIFIED ORGANISMS “Golden” rice-gene for Vitamin A added Bt-corn -resists insect pests

“frost resistant” strawberries toxin/pollution “eating” bacteria • ENDANGERED SPECIES ZOO cloning extinct/endangered species

PLASMIDS = small self replicating DNA loops • Can carry genes for ANTIBIOTIC RESISTANCE (used as genetic markers•Used as VECTORS to carry recombinant DNA •Can be cut with RESTRICTION ENZYMES •Used to incorporate foreign DNA into bacteria•Bacteria then reproduce, copying the inserted gene along with the plasmid

Ways to make bacteria able to “take up” foreign DNA = make them “ COMPETENT”

1) ELECTROPORATION- zap with electricity2) Use calcium chloride and “heat shock” to change their cell walls (We did this in LAB 8) - makes cells better able to pick up plasmids/DNA - rapidly growing cells are made competent more easilyGFP (Green Fluorescent Protein)•Originally discovered in jellyfish• Linked to plasmids carrying recombinant genes•Used as a genetic tool to identify presence of recombinant genes

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RESTRICTION ENZYMES (RESTRICTION ENDONUCLEASES)• Occur naturally in bacteria • Function = protect bacteria from invasion by foreign DNA• Each enzyme recognizes different specific code sequences ~often palindromes• Cut DNA into short segments with staggered “sticky ends”• Named for bacteria they come from: EX: EcoR1; HindIII; BamH1• DNA ligase used to join DNA pieces cut with same enzymes • Used to combine DNA from different organisms (recombinant DNA)

REVERSE TRANSCRIPTASE• Enzyme from RETROVIRUSES (RNA containing viruses) • info flows backwards RNA → DNA• Can be used to put eukaryotic genes into bacteria

• Bacteria don’t process DNA so eukaryotic genes with introns can’t be used directly• Reverse transcriptase enzymes can take n “edited” message and change it into a gene

GENE CLONING in BACTERIA•process used to produce multiple copies of specific segments of DNA• Isolate bacterial plasmid and foreign DNA•Treating with same restriction enzyme produces same “sticky ends”• Mix DNA•DNA ligase joins “sticky ends”• recombinant plasmid into taken up by bacteria (transformation)• bacteria reproduce resulting in multiple copies of the inserted gene

IDENTIFYING BACTERIA WITH RECOMBINANT PLASMIDS~Ability to grow in presence of antibiotics~ Presence of GFP (glow under UV light)

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GENE CLONING WITHPOLYMERASE CHAIN REACTION (PCR)Used to AMPLIFY DNAMakes billions of copies of even small quantities of DNANEED: target DNA, primers, nucleotides, & DNA Polymerase

Heat (94° C )- DNA helix unwinds/separates *Cool (54° C) - DNA hybridizes with primers and builds chain

Both strands of DNA are copied; then copied strands are used as templates in next round Heating/cooling process is repeated many times to get many copies

RFLP’s (RESTRICTION FRAGMENT LENGTH POLYMORPHISM) ANALYSIS inherited differences found among the

individuals in a population differences in DNA code result in different

restriction sites in DNA produces fragments of different lengths

= restriction fragment length polymorphisms (RFLP's) treat DNA with restriction enzymes use gel electrophoresis to separate the restriction fragments

AGAROSE GEL ELECTROPHORESIS = “swimming through JELLO”*** CAN BE USED TO SEPARATE ANY MOLECULE WITH A CHARGE ~ not just for DNA (Ex: proteins)•DNA is negatively charged (due to phosphates) so moves in electric field •Used to separate DNA fragments after cut with restriction enzymes•Separates by size and electric charge•Can identify DNA molecules by banding patterns•Can isolate and purify genes•DNA molecules can be identified by specific band patterns ~ separated by size and electric charge ~ DNA has + charge due to phosphates in backbone ~ Smaller fragments move farther ~ More voltage-move faster

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DNA DETECTION• ETHIDIUM BROMIDE- Glows under UV light but highly carcinogenic• METHYLENE BLUE DYE -see as blue bands• SOUTHERN BLOT -uses radioactively labeled probes to ID specific DNA segments

PROBLEM*HEAT destroys DNA PolymeraseSOLUTION: Use Taq POLYMERASE from hot springs archeabacteria (Thermus aquaticus) ~THERMOSTABILE-withstands 90° heat needed for strand separation


.

Build Your Own DNADescription:

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DNA DETECTION• ETHIDIUM BROMIDE- Glows under UV light but highly carcinogenic• METHYLENE BLUE DYE -see as blue bands• SOUTHERN BLOT -uses radioactively labeled probes to ID specific DNA segments


Using only home found materials, make a 3D model of a small segment of double stranded DNA.

Make sure to adhere to the following guidelines:

o Use only materials found in your house. Will I know if you go buy stuff? Probably not. But you will, and you will hate yourself for it.

o To thine own conceptually advanced model of DNA be true:

All parts of nucleotides! Base pairing! Hydrogen Bonding! Double helix (?)

o Include a key, explaining your model.o Don’t forget your name

These models will remain in this classroom. Maybe forever.

So make them pretty, or at the very least, make them something you won’t be ashamed of for the rest of the year!

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47


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DNA Analogy

Word Bank -you will use some words more than once

Let's pretend that you have a yen for a homemade Spanish omelet. The only recipe you know for that omelet is found in the Library of Spanish Cookery. There are many volumes of books in this specialized library and that recipe occurs on one page of one of those books. You can locate the library ____________________, the volume __________________ and page _____________________ on which the recipe is found.

The librarian (mean pants) refuses to let you check out the book as all reference material must stay in the library ______________________________. According to the rules of this library, photocopying _____________________________________ is out of the question as photocopying process in this library is only used if they have to recreate a duplicate library _____________________________.

You are free to transcribe the recipe_________________________ for the omelet ______________________________________ in your own handwriting on a piece of paper that is able to leave the library______________________. Remember you only used one opened page _______________________________ in the book.

You take this transcribed recipe_______________ for this omelet ____________________________ to a kitchen ___________________________ where you also bring your ingredients ______________________________ to be assembled _______________________ into an omelet _______________________according to the directions ______________________________. Not until your omelet is assembled in final form has your recipe __________________ been expressed ______________________.

The different ingredients are to be assembled in a particular order to result in the desired product. All omelets are always made in the kitchen____________________ and a mistake in the recipe ______________________________ can result in a poor tasting omelet.

Unwinds DNA double helix during replication

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DNA to mRNAMutationTranslationProteinNucleusGenetic diseaseChromosome

Amino acidsmRNA leaves the nucleusRibosomemRNAGeneCell divisionDNA is only found in the nucleus


Stabilize the unwound DNA strand at the replication fork

Enzyme that releases the tension in the twisted DNA strand as it unwinds by snipping the strand and resealing itAdds short RNA segments to which DNA polymerase III can attach nucleotides during replicationAdds deoxyribonucleotides to the 3’end of an existing chainRemoves RNA primers and replacesthem with deoxyribonucleotidesJoins Okazaki fragments on the lagging strandShort fragments made when the lagging strand is copied during replicationAdds segments to the ends of chromosomes to prevent shortening during replicationRecognizes splice sites and combines with proteins to form spliceosomesRNA molecules that function as enzymes

Editing complex containing “snurps” that removes introns and splices together exonsBinds to the promoter and adds ribonucleotides during transcriptionRegion on DNA where RNA polymerase bindsto start transcription

KNOW YOUR MOLECULES

DNA segment upstream from promoter that contains multiple control elements to speed up transcriptionBind to operator sites of operons to “turn off” genesPlace in an operon where the repressor binds to “turn off” a gene“death tag” that marks proteins for degradation

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by proteosomesBind to mRNA’s and tag them for digestion by ribonucleasesType of RNA made by the nucleolus;combines with proteins to make protein synthesis machinery (ribosomes)Type of RNA containing the codon sequence that is edited in eukaryotes before translationType of RNA containing the anticodon sequence that brings the correct amino acid into theribosomeCharges up tRNA’s by adding the correct amino acidAmino acid polymer produced by ribosomes during translation

CHAPTER 16-MOLECULAR BASIS OF INHERITANCE

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bacteriophage

DNA ligase

DNA polymerase

double helix

helicase

lagging strand

leading strand

mismatch repair

nuclease

nucleotide excision repair

Okazaki fragment

origin of replication

phage

primase

primer

replication fork

semiconservative model

single-strand binding protein

telomerase

telomere

topoisomerase

transformation

Word Roots

helic- a spiral (helicase: an enzyme that untwists the double helix of DNA at the replication forks)

liga- bound or tied (DNA ligase: a linking enzyme for DNA replication)

phage to eat (bacteriophages: viruses that infect bacteria)

semi- half (semiconservative model: type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule, and one newly made strand)

telos- an end (telomere: the protective structure at each end of a eukaryotic chromosome)

trans- across (transformation: a phenomenon in which external DNA is assimilated by a cell)

CHAPTER 17-FROM GENE TO PROTEIN

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5' cap

A site

alternative RNA splicing

aminoacyl-tRNA synthetase

anticodon

base-pair substitution

codon

deletion

domain

E site

exon

frameshift mutation

insertion

intron

messenger RNA (mRNA)

missense mutation

mutagen

mutation

nonsense mutation

one gene–one polypeptide hypothesis

P site

point mutation

poly-A tail

polyribosome (polysome)

primary transcript

promoter

reading frame

ribosomal RNA (rRNA)

ribosome

ribozyme

RNA polymerase

RNA processing

RNA splicing

signal peptide

signal-recognition particle (SRP)

spliceosome

TATA box

template strand

terminator

transcription

transcription factor

transcription initiation complex

transcription unit

transfer RNA (tRNA)

translation

triplet code

wobbleWord Roots

anti- opposite (anticodon: a specialized base triplet on one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule)

exo- out, outside, without (exon: a coding region of a eukaryotic gene that is expressed)

intro- within (intron: a noncoding, intervening sequence within a eukaryotic gene)

muta- change; -gen producing (mutagen: a physical or chemical agent that causes mutations)

poly- many (polyA tail: the modified end of the 39 end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides)

trans- across; -script write (transcription: the synthesis of RNA on a DNA template)

CHAPTER 19-EUKARYOTIC GENOME

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activator

alternative RNA splicing

cell differentiation

chromatin

control element

differential gene expression

enhancer

epigenetic inheritance

euchromatin

genomic imprinting

heterochromatin

histone

histone acetylation

microRNA (miRNA)

multigene family

nucleosome

oncogene

p53 gene

proteasome

proto-oncogene

pseudogene

ras gene

repetitive DNA

repressor

retrotransposon

RNA interference RNA (RNAi)

small interfering RNA (siRNA)

transcription factor

transposon

tumor-suppressor gene

Word Roots

eu- true (euchromatin: the more open, unraveled form of eukaryotic chromatin)

hetero- different (heterochromatin: nontranscribed eukaryotic chromatin that is so highly compacted that it is visible with a light microscope during interphase)

nucleo- the nucleus; -soma body (nucleosome: the basic beadlike unit of DNA packaging in eukaryotes)

proto- first, original; onco- tumor (proto-oncogene: a normal cellular gene corresponding to an oncogene)

pseudo- false (pseudogenes: DNA segments that are very similar to real genes but do not yield functional products)

retro- backward (retrotransposons: transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA)

CHAPTER 20-DNA TECHNOLOGY

biotechnology gene therapy proteomics

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cDNA library

clone

cloning vector

complementary DNA (cDNA)

denaturation

DNA fingerprint

DNA ligase

DNA microarray assay

electroporation

expression vector

gel electrophoresis

gene cloning

genetic engineering

genetically modified (GM) organism

genomic library

genomics

Human Genome Project

in vitro mutagenesis

linkage map

nucleic acid hybridization

nucleic acid probe

physical map

polymerase chain reaction (PCR)

recombinant DNA

restriction enzyme

restriction fragment

restriction fragment length polymorphism (RFLP)

restriction site

RNA interference (RNAi)

single nucleotide polymorphism (SNP)

Southern blotting

sticky end

Ti plasmid

transgenic

yeast artificial chromosome (YAC)

Word Roots

liga- bound, tied (DNA ligase: a linking enzyme essential for DNA replication)

electro- electricity (electroporation: a technique to introduce recombinant DNA into cells by applying a brief electrical pulse to a solution containing cells)

muta- change; -genesis origin, birth (in vitro mutagenesis: a technique to discover the function of a gene by introducing specific changes into the sequence of a cloned gene, reinserting the mutated gene into a cell, and studying the phenotype of the mutant)

poly- many; morph- form (single nucleotide polymorphism: one base-pair variation in the genome sequence)

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Molecular Genetics Student ObjectivesEnduring understanding 3.A: Heritable information provides for continuity of life.Essential knowledge 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information.

a. Genetic information is transmitted from one generation to the next through DNA or RNA.Evidence of student learning is a demonstrated understanding of each of the following:

1. Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules.

2. Noneukaryotic organisms have circular chromosomes, while eukaryotic organisms have multiple linear chromosomes, although in biology there are exceptions to this rule.

3. Prokaryotes, viruses and eukaryotes can contain plasmids, which are small extra-chromosomal, double-stranded circular DNA molecules.

4. The proof that DNA is the carrier of genetic information involved a number of important historical experiments. These include:

i. Contributions of Watson, Crick, Wilkins, and Franklin on the structure of DNAii. Avery-MacLeod-McCarty experimentsiii. Hershey-Chase experiment

5. DNA replication ensures continuity of hereditary information.i. Replication is a semiconservative process; that is, one strand serves as the template for a new, complementary strand.ii. Replication requires DNA polymerase plus many other essential cellular enzymes, occurs bidirectionally, and differs in the production of the leading and lagging strands.

b. DNA and RNA molecules have structural similarities and differences that define function. Evidence of student learning is a demonstrated understanding of each of the following:

1. Both have three components — sugar, phosphate and a nitrogenous base — which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3' and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone.

2. The basic structural differences include:i. DNA contains deoxyribose (RNA contains ribose).ii. RNA contains uracil in lieu of thymine in DNA.iii. DNA is usually double stranded, RNA is usually single stranded.iv. The two DNA strands in double-stranded DNA are antiparallel in

directionality.3. Both DNA and RNA exhibit specific nucleotide base pairing that is conserved

through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine (C-G).

i. Purines (G and A) have a double ring structure.ii. Pyrimidines (C, T and U) have a single ring structure.

4. The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.

i. mRNA carries information from the DNA to the ribosome.

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ii. tRNA molecules bind specific amino acids and allow information in the mRNA to be translated to a linear peptide sequence.

iii. rRNA molecules are functional building blocks of ribosomes.iv. The role of RNAi includes regulation of gene expression at the level of

mRNA transcription.c. Genetic information flows from a sequence of nucleotides in a gene to a sequence of amino acids in a protein.Evidence of student learning is a demonstrated understanding of each of the following:

1. The enzyme RNA-polymerase reads the DNA molecule in the 3' to 5' direction and synthesizes complementary mRNA molecules that determine the order of amino acids in the polypeptide.

2. In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications.To demonstrate student understanding of this concept, make sure you can

explain:i. Addition of a poly-A tailii. Addition of a GTP capiii. Excision of introns

2. Translation of the mRNA occurs in the cytoplasm on the ribosome.3. In prokaryotic organisms, transcription is coupled to translation of the

message. 5. Translation involves energy and many steps, including initiation, elongation and termination. The salient features include:

i. The mRNA interacts with the rRNA of the ribosome to initiate translation at the (start) codon.

ii. The sequence of nucleotides on the mRNA is read in triplets called codons.

iii. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids have more than one codon.

iv. tRNA brings the correct amino acid to the correct place on the mRNA.v. The amino acid is transferred to the growing peptide chain.vi. The process continues along the mRNA until a “stop” codon is reached.vii. The process terminates by release of the newly synthesized

peptide/protein.d. Phenotypes are determined through protein activities.To demonstrate student understanding of this concept, make sure you can explain:

Enzymatic reactions Transport by proteins Synthesis Degradation

Student Objectives: Explain how contributions from each of the following scientists led to an

understanding of DNA structure and function:o Griffitho Avery McCarty & McLeodo Hershey & Chaseo Erwin Chargaffo Watson, Crick, Franklin, & Wilkins

Diagram a molecule of DNA and explain how its features allow for both heredity and protein synthesis.

Explain how RNA and DNA differ in structure and function.

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Explain the role of mRNA, tRNA and rRNA in protein synthesis Explain the relationship between DNA, RNA, Protein, Cells and the

Organism. Explain the evidence that demonstrates the relationship between

phenotype and protein activity. Diagram the process of DNA replication. Discuss all inputs, processes, and

outputs. Explain the roles of all pertinent enzymes. Diagram the process of transcription. Discuss all inputs, processes, and

outputs. Explain the roles of all pertinent enzymes. Diagram the process of translation. Discuss all inputs, processes, and

outputs. Explain the roles of all pertinent enzymes, the ribosome, and relevant RNA molecules..

Compare replication, transcription, and translation among prokaryotes and eukaryotes. Explain the functions of all differences.

Learning Objectives: The student is able to construct scientific explanations that use the structures and

mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information.

The student is able to justify the selection of data from historical investigations that support the claim that DNA is the source of heritable information.

The student is able to describe representations and models that illustrate how genetic information is copied for transmission between generations.

The student is able to describe representations and models illustrating how genetic information is translated into polypeptides.

The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression.

Enduring understanding 3.B: Expression of genetic information involves cellular and molecular mechanisms.Essential knowledge 3.B.1: Gene regulation results in differential gene expression, leading to cell specialization.

a. Both DNA regulatory sequences, regulatory genes, and small regulatory RNAs are involved in gene expression.Evidence of student learning is a demonstrated understanding of each of the following:

1. Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription.To demonstrate student understanding of this concept, make sure you can

explain:i. Promotersii. Terminatorsiii. Enhancers

2. A regulatory gene is a sequence of DNA encoding a regulatory protein or RNA.b. Both positive and negative control mechanisms regulate gene expression in bacteria and viruses.Evidence of student learning is a demonstrated understanding of each of the following:

1. The expression of specific genes can be turned on by the presence of an inducer.

2. The expression of specific genes can be inhibited by the presence of a repressor.

3. Inducers and repressors are small molecules that interact with regulatory proteins and/or regulatory sequences.

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4. Regulatory proteins inhibit gene expression by binding to DNA and blocking transcription (negative control).

5. Regulatory proteins stimulate gene expression by binding to DNA and stimulating transcription (positive control) or binding to repressors to inactivate repressor function.

6. Certain genes are continuously expressed; that is, they are always turned “on,” e.g., the ribosomal genes.

c. In eukaryotes, gene expression is complex and control involves regulatory genes, regulatory elements and transcription factors that act in concert.Evidence of student learning is a demonstrated understanding of each of the following:

1. Transcription factors bind to specific DNA sequences and/or other regulatory proteins.

2. Some of these transcription factors are activators (increase expression), while others are repressors (decrease expression).

3. The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced.

d. Gene regulation accounts for some of the phenotypic differences between organisms with similar genes.

Student Objectives: Compare regulation of gene expression in prokaryotes and eukaryotes. Diagram inducible and repressible operons. Give examples of each. Compare the function of transcription factors and enhancers. Explain the structures, processes, and functions of regulation that operate

at all stages of gene expression in eukaryotes. Explain the relationship between gene expression and differentiation in

eukaryotes. Explain the relationship between gene expression and differences in

phenotypes in eukaryotes.

Learning Objectives: The student is able to describe the connection between the regulation of gene

expression and observed differences between different kinds of organisms. The student is able to describe the connection between the regulation of gene

expression and observed differences between individuals in a population. The student is able to explain how the regulation of gene expression is essential for

the processes and structures that support efficient cell function. The student can use representations to describe how gene regulation influences cell

products and function.Essential knowledge 3.B.2: A variety of intercellular and intracellular signal transmissions mediate gene expression.

a. Signal transmission within and between cells mediates gene expression.To demonstrate student understanding of this concept, make sure you can explain:

Mating pheromones in yeast trigger mating gene expression. Levels of cAMP regulate metabolic gene expression in bacteria.

Student Objectives: Using examples from cellular communication, explain how signal

transduction can effect gene expression in organisms.

Learning Objectives:

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The student is able to explain how signal pathways mediate gene expression, including how this process can affect protein production.

The student can use representations to describe mechanisms of the regulation of gene expression.

Enduring understanding 3.C: The processing of genetic information is imperfect and is a source of genetic variation.Essential knowledge 3.C.1: Changes in genotype can result in changes in phenotype.

a. Alterations in a DNA sequence can lead to changes in the type or amount of the protein produced and the consequent phenotype.Evidence of student learning is a demonstrated understanding of the following:

1. DNA mutations can be positive, negative or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein.

b. Errors in DNA replication or DNA repair mechanisms, and external factors, including radiation and reactive chemicals, can cause random changes, e.g., mutations in the DNA.Evidence of student learning is a demonstrated understanding of the following:

1. Whether or not a mutation is detrimental, beneficial or neutral depends on the environmental context. Mutations are the primary source of genetic variation.

Student Objectives: Explain the cause and effect of mutations at the DNA sequence level.

Provide examples of all types.

Learning Objectives: The student is able to predict how a change in genotype, when expressed as a

phenotype, provides a variation that can be subject to natural selection. The student can create a visual representation to illustrate how changes in a DNA

nucleotide sequence can result in a change in the polypeptide produced. The student is able to explain the connection between genetic variations in

organisms and phenotypic variations in populations.

Essential knowledge 3.C.2: Biological systems have multiple processes that increase genetic variation.

a. The imperfect nature of DNA replication and repair increases variation.b. The horizontal acquisitions of genetic information primarily in prokaryotes via transformation (uptake of naked DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer) and transposition (movement of DNA segments within and between DNA molecules) increase variation.

Student Objectives: Provide examples of all processes discussed in this course (to this point in

time) that illustrate the generation of genetic variation in prokaryotes and eukaryotes.

Learning Objectives: The student is able to compare and contrast processes by which genetic variation is

produced and maintained in organisms from multiple domains.

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The student is able to construct an explanation of the multiple processes that increase variation within a population.

Enduring understanding 3.A: Heritable information provides for continuity of life.Essential knowledge 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information.

a. Genetic information is transmitted from one generation to the next through DNA or RNA.Evidence of student learning is a demonstrated understanding of each of the following:

1. Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.

b. Genetic engineering techniques can manipulate the heritable information of DNA and, in special cases, RNA.To demonstrate student understanding of this concept, make sure you can explain:

Electrophoresis Plasmid-based transformation Restriction enzyme analysis of DNA Polymerase Chain Reaction (PCR)

c. Illustrative examples of products of genetic engineering include: Genetically modified foods Transgenic animals Cloned animals Pharmaceuticals, such as human insulin or factor X

Student Objectives: Describe the inputs, processes, and outputs of all biotechnological tools

and techniques discussed in this course. Provide multiple examples of the applications of each of these tools.

Explain the aspects of molecular biology and DNA that each tool and technique discussed in this course utilizes.

Discuss the ethical and legal considerations that the biotechnology revolution has generated. Provide multiple real-life examples of these issues. Offer multiple lines of evidence to support and refute these considerations.

Learning Objectives: The student is able to construct scientific explanations that use the structures and

mechanisms of DNA and RNA to support the claim that DNA and, in some cases, that RNA are the primary sources of heritable information.

The student can justify the claim that humans can manipulate heritable information by identifying at least two commonly used technologies.

The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression.

Enduring understanding 3.B: Expression of genetic information involves cellular and molecular mechanisms.Essential knowledge 3.B.2: A variety of intercellular and intracellular signal transmissions mediate gene expression.a. Signal transmission within and between cells mediates cell function.To demonstrate student understanding of this concept, make sure you can explain:

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Mating pheromones in yeast trigger mating genes expression and sexual reproduction.

Morphogens stimulate cell differentiation and development. Changes in p53 activity can result in cancer. HOX genes and their role in development.

Student Objectives: Explain the relationship between signal transduction and cellular

differentiation. Describe how morphogens and HOX genes contribute to the development of

an animal.

Learning Objectives: The student is able to explain how signal pathways mediate gene expression,

including how this process can affect protein production. The student can use representations to describe mechanisms of the regulation of

gene expression.

Enduring understanding 3.C: The processing of genetic information is imperfect and is a source of genetic variation.Essential knowledge 3.C.3: Viral replication results in genetic variation, and viral infection can introduce genetic variation into the hosts.

a. Viral replication differs from other reproductive strategies and generates genetic variation via various mechanisms. Evidence of student learning is a demonstrated understanding of each of the following:

1. Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes.

2. Viruses replicate via a component assembly model allowing one virus to produce many progeny simultaneously via the lytic cycle.

3. Virus replication allows for mutations to occur through usual host pathways.4. RNA viruses lack replication error-checking mechanisms, and thus have higher

rates of mutation.5. Related viruses can combine/recombine information if they infect the same

host cell.6. HIV is a well-studied system where the rapid evolution of a virus within the

host contributes to the pathogenicity of viral infection.b. The reproductive cycles of viruses facilitate transfer of genetic information.Evidence of student learning is a demonstrated understanding of each of the following:

1. Viruses transmit DNA or RNA when they infect a host cell. 2. To foster student understanding of this concept, instructors can choose an3. illustrative example such as:4. Transduction in bacteria5. Transposons present in incoming DNA6. Some viruses are able to integrate into the host DNA and establish a latent

(lysogenic) infection. These latent viral genomes can result in new properties for the host such as increased pathogenicity in bacteria.

Student Objectives: Diagram all modes of viral replication discussed in this course and provide

example viruses that follow each course of replication. Compare prokaryotic viruses and eukaryotic viruses.

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Explain the structure and function of HIV. Describe how viral processes increase genetic variation in prokaryotes and

eukaryotes. Diagram and describe the structure and function of transposons and

retrotransposons.

Learning Objectives: The student is able to construct an explanation of how viruses introducegenetic

variation in host organisms. The student is able to use representations and appropriate models to describe how

viral replication introduces genetic variation in the viral population.

Enduring understanding 4.A: Interactions within biological systems lead to complex properties.Essential knowledge 4.A.3: Interactions between external stimuli and regulated gene expression result in specialization of cells, tissues and organs.

a. Differentiation in development is due to external and internal cues that trigger gene regulation by proteins that bind to DNA. b. Structural and functional divergence of cells in development is due to expression of genes specific to a particular tissue or organ type. c. Environmental stimuli can affect gene expression in a mature cell.

Student Objectives: Explain the process of cellular divergence and differentiation. Provide examples of external and internal cues that direct divergence and

differentation.

Learning Objective: The student is able to refine representations to illustrate how interactions between

external stimuli and gene expression result in specialization of cells, tissues and organs.

Enduring understanding 4.C: Naturally occurring diversity among and between components within biological systems affects interactions with the environment.Essential knowledge 4.C.1: Variation in molecular units provides cells with a wider range of functions.

a. Multiple copies of alleles or genes (gene duplication) may provide new phenotypes. To demonstrate student understanding of this concept, make sure you can explain:

1. 1. A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses.

2. Gene duplication creates a situation in which one copy of the gene maintains its original function, while the duplicate may evolve a new function.To demonstrate student understanding of this concept, make sure you can

explain: The antifreeze gene in fish

Student Objectives: Describe the evolutionary processes that are seen in genomic analysis and

how these processes affect the structure of genomes.

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Explain the structure and function of all major segments of the human genome.

Explain how gene duplication can lead to an increase in genetic information in an organism.

Cite evidence from genomic analysis that relates to the evolution of the human lineage.

Learning Objective: The student is able to construct explanations based on evidence of how variation in

molecular units provides cells with a wider range of functions.

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eukaryotic genome regulation-genes not...

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