name: block: date: unit 4: cell development and...

Biology Honors 2014-2015

Name: ____________________________________ Block:________ Date:________________________ PACKET #9 !

Unit 4: Cell Development and Replication, Part II: Gene Expression !Reading: Chapter 9, plus 14.1 and 15.4 !Objectives: By the conclusion of this unit the student will be able to: !12. Define “genes” and explain their function and importance (9.1). 13. Explain the functions of DNA, mRNA, tRNA, rRNA, and Proteins (9.1). 14. Explain what is meant by the “genetic code,” including the role of codons and anticodons (9.1). 15. List at least three functions that proteins have in cells (9.2). 16. List the structural differences between DNA and RNA (9.3). 17. Describe the process of RNA synthesis during transcription (9.3). 18. Explain how the RNA transcript is processed to become mRNA (9.4). 19. Describe the process of translation (9.5). 20. Explain how proteins are transported and processed (post translational modifications)(9.6). 21. Describe the types of mutations (translation errors) and how they can affect protein structure (9.7, 15.4) 22. Explain how all cells in an organism have the same DNA but different cells manufacture different proteins

and serve different functions (page 240, 14.1) !!!Vocabulary: Transcription Translation Protein synthesis Genetic Code Messenger RNA Transfer RNA Ribosomal RNA Ribosome Codon Anticodon

RNA polymerase RNA processing Initiation Elongation Termination Signal sequence Mutation Frameshift mutation Splicing Introns/Exons

Promotor Transcription Factor Start and Stop codons Coding strand Template strand Reading frame Point mutation Missense mutation Nonsense mutation Central Dogma !!!

!1


!2

What%is%a%Gene?%%%Figure'1:'Locating'a'Gene'

''Figure'2:'A'Simplified,'Completely'Fictional'Chromosome'Map''Humans'have'23'pairs'of'chromosomes.'A'single'pair'is'shown'here.''Why'pairs?'Because'one'set'of'genes'come'from'each'parent.'''

'

''Figure'3:'Central'Dogma'of'Molecular'Biology''Arrows'in'this'diagram'show'a'transfer'of'information.'Notice'that'proteins'are'the'final'product.'Once'information'gets'into'the'form'of'protein,'it'cannot'get'out'again''

'

Define'gene:''

Relate'the'terms:'chromosome,'genes:''

gene'for'making'earwax'

gene'for'eye'color'

gene'for'hitchhiker’s'thumb'

gene'for'freckles'

gene'for'dimples'

How'do'genes'code'for'life?'''


!

!3

From%DNA%to%Proteins%Web%Quest%%Log%on%to%http://learn.genetics.utah.edu/.%Explore%this%module%to%find%the%answers%to%the%questions%below.%%

%Follow the links: Home ! Molecules of Inheritance ! RNA the versitile molecule %1.##Fill#in#the#table#below#to#explain#several#similarities#and#differences#between#DNA#and#RNA.##Similarities% Differences%Both%DNA%and%RNA%have…% DNA%has…% RNA%has…%1.##

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2.#

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3.#

1.#

2.#

3.#

4.##

5.#

1.#

2.#

3.#

4.#

5.#

#2.##How#does#the#singleBstranded#nature#of#RNA#allow#for#endless#possible#shapes#and#functions?### Molecules of Inheritance ! Anatomy of a Gene 3.##IN#YOUR#OWN#WORDS,#describe#the#function#of#each#of#the#following#regions#of#a#gene:#

Promoter#

Switch#(DNA#sequence)#

Switch#(Protein)#

Start#Codon#

Exon#

Intron#

Stop#Codon#

%

Optional:#For#a#quick#review#of#the#topics#we’ve#covered#so#far,#check#out#“A%Tour%of%the%Basics”.##Here#you#will#find#quick,#helpful#tutorials:#

• What#is#DNA?#• What#is#a#gene?#• What#is#a#chromosome?#• What#is#a#protein?#


!4

Molecules of Inheritance ! Proteins ! What is a protein %4.##What#role#do#receptor#proteins#play#in#the#sending#of#nerve#signals#throughout#the#body?###5.##How#do#proteins#relate#to#the#unique#shape#of#nerve#cells?#####6.##Recall#from#our#“Cells”#unit:#How#does#the#finished#protein#migrate#to#its#ultimate#destination?#

What#organelles#are#involved?#######Molecules of Inheritance ! Proteins ##! Types of proteins #7.###Match#the#specific#protein#to#its#function:##_______##Egg#white#protein;#energy#source#for#developing#bird#

_______##Allow#for#contraction#(movement)#of#muscle#cells#

_______##Food#source#for#germinating#wheat#plant#

_______##Carry#vessicles#around#inside#a#cell#

_______##Prevents#cell#from#dividing#when#DNA#is#damaged#

_______##Digestion#of#milk#sugar#

_______##Strong,#stretchy#protein#found#in#tendons#and#ligaments#

_______##Builds#DNA#molecules#

_______##Transports#oxygen#in#red#blood#cells#

_______##Energy#production;#part#of#electron#transport#chain#in#

mitochondria#

_______##Helps#decrease#blood#sugar#after#a#meal;#sugar#is#taken#up#by#cells#

_______#Wound#healing;#initiates#cell#division#in#skin#cells#

%%Home ! Genetic Variation ! Test Neurofibromin Activity in a Cell 8.##Describe#the#functions#of#neurofibromin#and#the#Ras#protein.#####9.##How#might#a#DNA#mutation#in#the#Ras#gene#or#the#NF1#gene#affect#the#function#of#these#proteins?#(Be#specific.)######

A. Gluten B. Epidermal growth

factor (EGF) C. Myosin & actin D. p53 E. Collagen F. DNA Polymerase G. Hemoglobin H. Ovalbumin I. Cytochrome C J. Lactase K. Dyenin L. Insulin


!5

Home ! Molecules of Inheritance ! Proteins ! Prions %10.##What#is#a#prion?##

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11.##Give#a#few#examples#of#prionBrelated#diseases.##

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12.##How#do#prions#cause#spongiform#diseases?#(You#will#find#this#information#by#watching#the#slideshow.)#

Home ! Molecules of Inheritance ! The Time of our Lives 13.##What#are#Circadian#Rhythms?##

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14.##What#part#of#the#human#brain#is#involved#in#“telling#time”?#What#external#cues#does#this#brain#region#use?##

##

15.$$Per$and$tim$genes#code#for#PER#and#TIM#proteins#in#fruit#flies.#How#do#these#PER#and#TIM#proteins#work#together#with#CLK#and#CYC#proteins#to#serve#as#an#internal#clock#for#the#fly?##

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# At#what#times#are#CLK#and#CYC#proteins#found#in#the#cell?###

## What#do#CLK#and#CYC#proteins#do#when#they#are#functioning?#

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## At#what#times#are#PER/TIM#protein#complexes#found#in#the#cell?##

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## What#effect#does#the#PER/TIM#complex#have#on#the#CLK#and#CYC#proteins?##

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16.##On#the#axes#below,#graph#the#relative#levels#of#both#protein#complexes#throughout#a#24Bhr#

period.###

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Time

- - - CYC/CLK complex ____ PER/TIM complex

Prot

ein

conc

entra

tions

M

in

m

ax

12am 4am 8am 12pm 4pm 8pm 12am


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Gene Expression—Transcription 1

Gene Expression—TranscriptionHow is mRNA synthesized and what message does it carry?

Why?DNA is often referred to as a genetic blueprint. In the same way that blueprints contain the instructions for construction of a building, the DNA found inside the nuclei of cells contains the instructions for assembling a living organism. The DNA blueprint carries its instructions in the form of genes. In most cases the genes direct the production of a polypeptide, from which other more complex proteins, such as enzymes or hormones, may be constructed. These polypeptides and other molecules run the organism’s metabolism and, in multicellular organisms, dictate what each cell’s job is. So, what is the language of these instructions and how are they read and decoded by the cellular organelles? This activity will focus on the decoding of genes in eukaryotes.

Model 1 – Transcription

Template (reading) strand

RNA polymerase andtranscription factors

A

AA

A

A

AC

C

C

C

C

CC

G

G

G

G G

G

G

T

U

U

A

A C G

G G

G AC

C

AInside the Nucleus

Nuclear membraneFree RNAnucleotides

Outside the N

ucleus

Growing strand of pre-mRNADirection of synthesis

3´5´

3´5´Chromosome from anondividing cell

U

UU

U U

U

U

U


!7

2 POGIL™ Activities for AP* Biology

1. Consider the eukaryotic cell in Model 1.

a. Where in the cell is the DNA found?

b. Where in the cell does transcription take place?

2. Refer to Model 1.

a. What polymer is synthesized during transcription?

b. What monomers are used to construct this polymer and where are they found?

3. According to Model 1, what enzyme is required for transcription? (Hint: Think about how enzymes are named. What ending is used for enzyme names?)


a. What is the base-pair rule for a DNA strand matching an RNA strand?

b. Compare this base-pair rule with that of two DNA strands.

5. Which strand of the DNA contains the “blueprint” for the pre-mRNA?

6. Consider Model 1.

a. In which direction is the DNA molecule read?

b. The DNA strand and pre-mRNA strand are anti-parallel. With this in mind label the 3v and 5v ends of the pre-mRNA strand in Model 1.

c. In which direction is the pre-mRNA molecule constructed?

7. Before printing presses were available, books had to be transcribed in order to share the informa-tion in them. Consider the defi nition of transcription and explain why the process in Model 1 is described using that word.


!84 POGIL™ Activities for AP* Biology

Model 2 – mRNA Processing

A

A

C

C

G

G

U

U

U

G

G

A

C

C

A

A

A

C

C

G

G

U

U

U

G

G

A

C

C

A

Leading intron

Start codonIntron

Intron

Intron

Inside theNucleus

Outside theNucleus

Nuclear pore

A

UG

C

UU

G

G

GC

CCA A U U AA

Poly-A tail

A A AA AA A

Methyl cap

5´

Pre-mRNA

mRNA

Exon

Exon

Exon

3´

12. Compare the pre-mRNA to the mRNA leaving the nucleus in Model 1.

a. What has been removed from the pre-mRNA to make it into mRNA?

b. What has been added to the mRNA that was not present in the pre-mRNA, and where on the mRNA strand are the additional items located?

13. Identify the structure through which the mRNA leaves the nucleus.

14. The nucleotides on the mRNA will be “read” in the next step to producing a polypeptide. What sequence of bases indicates the starting point for the polypeptide “blueprint”?

15. The “m” in mRNA is short for “messenger.” Why is this molecule called messenger RNA?


!9Gene Expression—Transcription 5

Read This!Introns are sections of pre-mRNA that are noncoding. That is, they don’t provide useful information for the production of the polypeptide being synthesized. There is evidence that suggests these introns al-low certain sections of DNA to code for different polypeptides when different sections are removed. The removal of specifi c sections is triggered by a signal response in the cell. The portions of the pre-mRNA that remain are called exons. The methyl cap (sometimes called the GTP cap or 5v cap) helps the mRNA molecule move through the nuclear pore and attach to a ribosome, its fi nal destination. mRNA is a short-lived molecule. Once in the cytoplasm the mRNA will be subject to exonucleases that immediately start removing individual nucleotides from the 3v end of a nucleic acid. The individual mRNA nucleotides will then be free to be used again during the process of transcription.

16. The human genome contains about 25,000 genes and yet produces about 100,000 different polypeptides. Propose an explanation of how this is possible.

17. Using the information in the Read This! box, develop a hypothesis to explain the advantage of the poly-A tail added to the 3’ end of the mRNA.

18. Different mRNA molecules can have poly-A tails of different lengths. Considering the purpose of adding the poly-A tail (from the previous question), why are some tails longer than others? Justify your answer using complete sentences.

19. Summarize the steps of transcription.


!10Gene Expression—Translation 1

Gene Expression—TranslationHow do cells synthesize polypeptides and convert them to functional proteins?

Why?The message in your DNA of who you are and how your body works is carried out by cells through gene expression. In most cases this means synthesizing a specific protein to do a specific job. First, mRNA is transcribed from the DNA code. Then, the mRNA sequence is translated into a polypeptide sequence.

Model 1 – CodonsmRNA nucleotides Amino acids

Second Base

U C A G

Firs

t Bas

e

UUUU PheUUC PheUUA LeuUUG Leu

UCU SerUCC SerUCA SerUCG Ser

UAU TyrUAC TyrUAA stopUAG stop

UGU CysUGC CysUGA stopUGG Trp

UCAG

Third B

ase

CCUU LeuCUC LeuCUA LeuCUG Leu

CCU ProCCC ProCCA ProCCG Pro

CAU HisCAC HisCAA GlnCAG Gln

CGU ArgCGC ArgCGA ArgCGG Arg

UCAG

AAUU IleAUC IleAUA Ile

AUG Met (start)

ACU ThrACC ThrACA ThrACG Thr

AAU AsnAAC AsnAAA LysAAG Lys

AGU SerAGC SerAGA ArgAGG Arg

UCAG

GGUU ValGUC ValGUA ValGUG Val

GCU AlaGCC AlaGCA AlaGCG Ala

GAU AspGAC AspGAA GluGAG Glu

GGU GlyGGC GlyGGA GlyGGG Gly

UCAG

1. Model 1 defines the code scientists have discovered that relates the nucleotide sequence of mRNA to the amino acid sequence of polypeptides.

a. What do the letters U, C, A, and G in Model 1 represent?

b. What do the abbreviations such as Phe, Ile, Ala, and Gly in Model 1 represent?

c. The language of mRNA is often described as a “triplet code.” Explain the significance of this reference.

Gene Expression—Translation 3

Model 2 – Translation

AU CCCC AA AAGGGG UU UU

mRNA5´ 3´

U CA

Met

CAA

LeuUG A

His

CU G

Ser

G GC

AlaAmino acid

ChargedtRNA

Anticodon

Ribosome


CAA

Leu

UG A

His

CU G

Ser

G GC

Ala

U CA

Met

UnchargedtRNA


UCA

Met

A CA

Leu

UG

A

His

CU

G

Ser

GG

C

Ala H2O

Releasefactor

Initiation Elongation

Termination


a. What are the three stages of translation?

b. Define each of the terms used in your answer to part a as they are used in everyday language.


!114 POGIL™ Activities for AP* Biology

8. According to Model 2, when the mRNA leaves the nucleus, to which cellular organelle does it attach?

9. The mRNA attaches to the organelle at the sequence AUG. What is the signifi cance of this sequence of nucleotides?

10. Describe the movement of the ribosome as translation occurs.

Read This!The ribosome is a large complex of ribosomal RNA (rRNA) and proteins. It consists of two subunits. The smaller subunit binds to the mRNA strand and the larger subunit holds the tRNA molecules in place while the covalent peptide bond is formed between the amino acids. Several ribosomes can attach to an mRNA molecule simultaneously. This allows for many polypeptide chains to be synthesized at once.

11. The tRNA molecules in a cell are short sequences of nucleotides (about 80 bases) that contain an anticodon and carry a specifi c amino acid.

a. Find the tRNA in Model 2 that is carrying the Histidine (His). What sequence of nucleotides makes the anticodon on this tRNA molecule?

b. What codon on mRNA would match this anticodon?

c. Verify that the codon you wrote in part b codes to Histidine by looking at the table in Model 1.

d. What anticodon would be found on a tRNA molecule carrying Glycine (Gly)? (Note: There are several correct answers here.)

12. The “t” in tRNA is short for transfer. In a complete sentence, explain why this molecule is called transfer RNA.


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Gene Expression—Translation 5

13. During elongation, how many tRNA molecules are held in the ribosome at the same time?

14. What will happen to the unattached tRNA once it has delivered its amino acid?

15. Describe two things that occur during termination as illustrated in Model 2.

16. Explain how the term “translation” applies to the synthesis of proteins from DNA instructions.

6 POGIL™ Activities for AP* Biology

Extension Questions17. The codons of mRNA are a set of three nucleotides with four possible bases in combination.

a. Show mathematically that there are 64 permutations possible when three bases are used.

b. Show mathematically that two bases as a codon would not be sufficient to code for all 20 known amino acids.

18. A silent mutation is one that does not affect protein structure. Write a code for an original DNA strand containing at least 12 bases, and then mutate the original DNA so that the final protein is unaffected.

19. In prokaryotic cells, translation begins before transcription is finished. Give two reasons why this would not be possible in eukaryotic cells.


!13

Regulating Gene Expression

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WHICH PROTEINS? HOW MANY OF EACH?

•  Gene expression is controlled at many different stages along the way from DNA to RNA to protein!

•  It’s important to have exactly the right amount of each protein for a cell to function normally.

•  Different cells are specialized and must produce different proteins.

POST-TRANLATIONAL PROCESSING

1. New polypeptides must be folded •  Functional proteins have 1o, 2o, 3o and 4o structure •  The translated amino acid sequence is 1o

•  The new polypeptide is not functional, yet.

WHAT GUIDES FOLDING?

•  2o is spontaneous due to H-bond formation within backbone. •  Chemical properties of amino acids ! 3o structure

Chaperone proteins help with tertiary and quaternary levels of folding

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2. Proteins need modifications: A new polypeptide may be cleaved, bound to other polypeptides and/or modified by the addition of functional groups.

3. Proteins must be delivered to their site of action: secreted by exocytosis, or delivered to membranes, cytoplasm or nucleus. 5’ signal sequence

REVIEW: HOW A PROTEIN IS BORN!

•  Chromatin remodeling •  Transcription •  mRNA processing •  mRNA stabilization to some degree •  Translation •  Post translational modification •  Delivery to site of action

•  * Proteins, like mRNAs have different lifespans. A final factor in gene expression is how long the protein lasts

•  Genome: All of the DNA in a cell of an organism. Every cell in an organism has a nearly identical genome.

•  Proteome: All of the proteins in an organism. •  Humans have ~ 20,000 genes, but many times more

proteins •  The old rule was One Gene ! One Protein •  New Rule: One gene ! one, two, seven ... many

proteins!

PROTEOME >> GENOME


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Review Questions: 1. How do cells differentiate (specialize), when all cells in your body have the same exact DNA? 2. What would happen to the level of gene expression in each of the following situations?

The mature mRNA is rapidly broken down after it has been synthesized. Transcription factors and histone modification allow for many mRNA copies of a gene. A protein resists being broken down in the cytoplasm, which results in a long lifespan for this protein.

3. What are chaperone proteins? What do they do? 4. How does the production of a cytoplasmic protein differ from production of a hormone? How does

the cell know where to send these different proteins? 5. Describe two ways that a single mRNA molecule may be used to build multiple different proteins.

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2. Proteins need modifications: A new polypeptide may be cleaved, bound to other polypeptides and/or modified by the addition of functional groups.

3. Proteins must be delivered to their site of action: secreted by exocytosis, or delivered to membranes, cytoplasm or nucleus. 5’ signal sequence

REVIEW: HOW A PROTEIN IS BORN!

•  Chromatin remodeling •  Transcription •  mRNA processing •  mRNA stabilization to some degree •  Translation •  Post translational modification •  Delivery to site of action

•  * Proteins, like mRNAs have different lifespans. A final factor in gene expression is how long the protein lasts

•  Genome: All of the DNA in a cell of an organism. Every cell in an organism has a nearly identical genome. •  Proteome: All of the proteins in an organism. •  Humans have ~ 20,000 genes, but many times more

proteins •  The old rule was One Gene ! One Protein •  New Rule: One gene ! one, two, seven ... many

proteins!

PROTEOME >> GENOME

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PROTEOME >> GENOME


Transcription and Translation Homework! !1. Define codon and anticodon: !!!!Directions: Using your Amino Chart (Pink Sheet), fill out the organizer on page 16. !1. Using the sequence of the DNA strand in the second column as a template, write the letter for the

corresponding nucleotide in the mRNA. !2. From position 11 thru 76, write the letter for the corresponding nucleotide in the tRNA anticodon. !3. Translate the codons in the mRNA column into amino acids. Enter the three letter amino acid code

in the final column. !!Analysis: !1. Why do the tRNA and amino acid columns start at position 11 and end at position 76? !!!!!2. Rewrite the first 10 nucleotides of the DNA sequence in a straight line below. Above it write the

letters of the nucleotides for the opposite DNA strand. What is the relationship between the mRNA sequence and the sequence of the DNA strand that is not copied? !!!!!

3. What is the relationship between the sequence of the tRNA anticodon and the sequence of the DNA strand that is copied? !!!!!!!!!

!15


Mutations! !4. Change the “G” at position 31 to an “A”. What effect does this change have on the amino acid

sequence? What effect is this change in the DNA likely to have on the protein? !!!!!5. Now change the same “G” to a “C”. What effect does this change have on the amino acid sequence?

What effect is this change in the DNA likely to have on the protein? !!!!!6. Now change the “C” at position 37 to a “T”. What effect does this change have on the amino acid

sequence? What effect is this change in the DNA likely to have on the protein? !!!!STOP HERE. Complete the Mutations Card Sort Activity before moving on. Using your newly filled-in mutations chart, categorize the mutations you categorized above and explain your answer. !The mutation described in #4: !!!!!!The mutation described in #5: !!!!!!The mutation described in #6: !

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Position

DNA strand to be copied mRNA

tRNA anticodon amino acid

1 C 2 G 3 T 4 C 5 A 6 A 7 A 8 C 9 T 10 G 11 T 12 A 13 C 14 C 15 C 16 G 17 A 18 T 19 A 20 T 21 T 22 T 23 T 24 G 25 T 26 A 27 A 28 A 29 G 30 T 31 G 32 C 33 C 34 G 35 A 36 C 37 C 38 A 39 G 40 G 41 T 42 A 43 A


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Position

DNA strand to be copied mRNA

tRNA anticodon amino acid

44 T 45 A 46 G 47 G 48 G 49 C 50 T 51 G 52 T 53 A 54 A 55 C 56 T 57 G 58 T 59 A 60 A 61 A 62 G 63 G 64 G 65 G 66 T 67 G 68 T 69 A 70 A 71 T 72 G 73 G 74 A 75 C 76 T 77 A 78 C 79 G 80 T 81 T 82 A 83 T 84 T 85 C 86 G


!! Mutations Chart

!19


Gene, Proteins, and Disease!Adapted from BSCS: The Human Approach, page 458-464!!Introduction: You have studied how a DNA molecule can act as a template for its own replication. Genetic information is used to build and maintain the physical characteristics of an organism. But how is the information in DNA used within the cell to produce those characteristics? How is the message in the DNA nucleotide sequence translated into a physical characteristic? !! In this activity you will model the relationship between DNA and RNA for a particular trait. You will also identify the connection between a DNA sequence and the end protein product. The gene you will study is that for sickle-cell disease. !(1 pt)!Transcription!!!!Translation!!!!!Process and Procedure!!Part 1: Learning about Sickle-Cell Disease!1.! Read the attached “Need to Know part 1” section on Hemoglobin and Red Blood Cell Abnormalities

in Sickle-Cell Disease (later in the packet – p 9).!2.! Read the essay “Incomplete Dominance” later in the packet (p 8). What might the phenotype be for

a person with the genotype HbAHbS? (1 pt)!!!3.! Discuss and record answers to the following questions. (0.5 pt each)!

a.! What medical symptoms might a person with sickle-cell disease experience?! !!!!b.! What problem in shape and behavior the red blood cells causes these symptoms to happen?! !!!c.! What problem in the behavior of the hemoglobin molecules is associated with these changes

in an individual’s red blood cells?!!!!d.! Think back to your knowledge of DNA structure. What might be the molecular basis for the

physical characteristics of sickle-cell disease (in other words – what makes one person’s DNA for this gene different from another person’s DNA)?!!

!20


4.# Use#the#information#gathered#to#2ill#in#the#genotype#and#sections(6,(7,(8,(and(9#of#both#parts#of####your#separate#Gene(Expression(Planner.##(Don’t#just#use#drawings!##Write#something#too!#And#take#note#of#“normal”#and#“sickle”#at#the#top#of#the#page!!)#These#are#the#physical#results#of#the#sickleFcell#gene.##Now#let’s#look#at#the#underlying#molecular#cause#for#these#physical#traits.##Get#a#stamp#before#moving#on.#!!

Part 2: Modeling Transcription – formation of mRNA!To begin this section, you must show the teacher you gene expression planner with parts 6, 7 and 8 filled in. !!5.! Write out the complimentary strand of DNA using the sequence below. Get a stamp before moving

on to step 6. (1 pt)!!!! ! ! Gene: T A C C A C G G G A T T!

! ! Complimentary DNA Strand:! !6.! The formation of an mRNA is very similar to the process of DNA replication. The enzyme RNA

polymerase opens up the DNA double helix and starts building a new complementary strand. However, unlike DNA replication, which uses both strands, RNA polymerase only uses one strand of DNA, called the template. Also, the new strand is made of RNA nucleotides instead of DNA nucleotides. !!

7.! Use the gene strand above as a template to write out a single mRNA molecule. (The RNA base uracil replaces the DNA base thymine.) After RNA polymerase forms the mRNA strand, it detaches from the gene strand and the two DNA strands reconnect. Remember - the DNA molecule ALWAYS remains in the nucleus. Now the DNA is safe in the nucleus and RNA can go to the cytoplasm to assist in making protein. Record the sequence of your mRNA strand in the space below. Get a stamp before moving on to step 9. (1 pt)!!!!

Gene: T A C C A C G G G A T T!mRNA Strand:!!

Part 3: Examining the DNA sequence of Hemoglobin !8.! Below are the sections of the DNA sequences of a normal hemoglobin gene and the mutated gene

that causes Sickle-cell disease. The sequences for these have been written in box 2 of your Gene Expression Planner. In box 2, write the complementary DNA sequence.!!Normal Gene!…GTGCACCTGACTCCTGAGGAG… !Mutated Gene!…GTGCACCTGACTCCTGTGGAG… !

!21


9.! On your planner (both pages), in box 2, circle or draw an arrow to indicate the nucleotide(s) in the sickle-cell sequence that differs from those in the normal sequence. !!

10.#In(box(3,#transcribe#the#message#into#the#mRNA#sequence.#Use#the#complementary#sequence#that#you#recorded)##Refer#back#to#your#procedure#from#Part#2.##How#did#you#form#the#mRNA#there?##Do#the#same#thing#here!##Check#with#your#teacher#before#moving#on#to#the#next#step.#

!11.!Refer to the genetic code diagram handout. Use the table to determine the sequence of amino acids

that would result from translating the mRNA that you built from your complementary DNA sequence. Put your resulting amino acid sequence into box 4 on your gene expression planner. To complete this step, you will need more information about the genetic code and how mRNA is translated into protein. Refer to your notes from Section III of the reading guide (Textbook – 12.3) and the genetic code chart below.!!!!

12.!In box 4, draw a circle or arrow to indicate the amino acid(s) in the sickle-cell protein sequence that differs from those in the normal sequence.!!

13.!Read the attached “Need to Know part 2” section (packet p 10) on The Sequence of Amino Acids Determines the Hemoglobin Molecule’s Shape. Use what you learn to fill in position 5 on your planner, also use what you have learned to add to positions 6, 7, and 8 if necessary. Again – don’t just draw! Use words to describe the differences!!!!!

!

!22


Analysis Questions (discuss with your groups while you answer these)!!1. How does the shape of the protein cause the symptoms of sickle-cell disease? !!!!!2. What ultimately controls the shape and function of proteins? !

3. Explain how a mutation in a DNA sequence affects a physical trait. How is the mutated message transferred through the process of transcription and translation? !!!!!

4. The mutations you have looked at in this activity all occurred in the original DNA sequence. How do you think they got there? !!!!!

5. Can you think of other ways mutations might occur? In other words, how might a protein be mutated if the DNA is not? !!!!!

6. The amino acid code is said to be redundant but not ambiguous. Look at your wheel and hypothesize what this means. Why might this be advantageous to life? !!

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NEED TO KNOW PART 1 !Hemoglobin and Red Blood Cell Abnormalities in Sickle-Cell Disease !

Each year, about one in 625 African American children is born with sickle-cell disease. This disease is caused by an abnormality in hemoglobin. Hemoglobin is the protein in red blood cells that carries oxygen to body cells. When the oxygen supply in the blood is low, these abnormal hemoglobin molecules clump together. Normal hemoglobin molecules remain separate. Figure 1 shows the difference between the behavior of sickle-cell hemoglobin and normal hemoglobin under conditions of low oxygen.

In a person with sickle-cell disease, the clumping of the hemoglobin molecules at low oxygen levels causes the red blood cells to become long and rigid like a sickle instead of remaining round and flexible (Figure 2). That change in cell shape causes a variety of problem in the body. For example, as cells become sickled, they tend to block small blood vessels (Figure 3). This causes pain and damage to the areas that do not receive an adequate blood supply. The long-term effect of repeated blockages may permanently damage a person’s internal organs. This includes the heart, lungs, kidneys, brain, and liver. For some people, the damage is so severe that they die in childhood. With good medical care, however, many people with sickle-cell disease can live reasonably normal lives.

Sickle-cell disease is associated with the genotype HbsHbs. People who have this condition have two abnormal genes, one inherited from each parent. !!!

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Figure'3.'Comparison'of'movement'of'normal'(le6)'and'sickle;cell'(right)'red'blood'cells'through'blood'vessels.

Figure'2.'Comparison'of'the'shapes'of'abnormal'sickle;cell'(le6)'and'normal'(right)'red'blood'cells'under'condi?ons'of'low'oxygen.

!!!!!normal!!! !!!!!!!!!!!!!!!!low!!!!!!oxygen!level! !!!!!!!!oxygen!level!!

normal!hemoglobin

!!!!!normal!!! !!!!!!!!!!!!!!!!low!!!!!!oxygen!level! !!!!!!!!oxygen!level!!

sickle!hemoglobin

Figure'1.'Comparison'of'the'behavior'of'normal'and'sickle;cell'hemoglobin'under'condi?ons'of'low'oxygen.


!NEED TO KNOW PART 2 !The Sequence of Amino Acids Determines the Hemoglobin Molecule’s Shape !

Inside the environment of a red blood cell, a molecule of normal hemoglobin consists of four protein chains folded into a globular shape. The molecule remains folded in this manner because attractive forces occur between amino acids in different parts of the molecule’s protein chains.

A change in the amino acid sequence can take place because of the single nucleotide mutation in the hemoglobin gene. This, however, has no effect on the molecule’s overall shape when oxygen levels are normal. For that reason, sickle-cell hemoglobin behaves just like normal hemoglobin under such conditions.

When oxygen levels are low, however, the change in a single amino acid alters the attractive forces inside the molecule. That causes molecules of sickle-cell hemoglobin to assume a different shape from those of normal hemoglobin. As Figure 4 shows, it is the change in molecule shape under low oxygen levels that causes sickle-cell hemoglobin to form the rigid rods characteristic of the condition. Don't forget to look at the figure and read the figure caption! !!!DON’T FORGET TO READ THE CAPTION BELOW!!! !Figure 4. Normal and sickle hemoglobin. The difference in behavior of sickle-cell hemoglobin is related to a change in shape that takes place at low oxygen levels. This shape change results from the amino acid valine replacing a glutamic acid. (a) Molecules of normal hemoglobin will not associate with each other. This is because the bulge created by the glutamic acid is too large to fit into a pocket in another hemoglobin molecule. Molecules of sickle hemoglobin, however, will associate with each other. This is because the bulge created when valine replaces glutamic acid is small enough to fit into the pocket. (The size of the pocket does not change.) (b) Molecules of normal hemoglobin remain in solution, even under conditions of low oxygen. In contrast, molecules of sickle hemoglobin associate together to form rigid cells under low oxygen conditions. !

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DNA Practice Questions !Part I: Fill-in-the-Blank 1. Transcription occurs in/at the _____________ (what part of the cell?), and is when single-stranded DNA is

used as a template with which to build ___________. Transcription is catalyzed by an enzyme called ____________________. !

2. Translation occurs in/at the ______________ (what part of the cell?), and is when mRNA is used as a template with which to build _____________. !

3. If you had 999 nucleotides (assume no non-coding sequences), you would expect a protein sequence of ______ (how many?) amino acids. !

Part II: Word Relationships In each of the following sets, one word does not belong. Circle the one that doesn’t belong, and explain why it doesn’t belong. 4. deoxyribose, phosphate, DNA, uracil 5. amino acid, polypeptide, protein, transcription 6. ribose, RNA, thymine, adenine 7. A-T, G-G, A-U, C-G !Replace the underlined definition with the correct vocabulary word. 8. The attraction between nitrogenous bases is the force that holds the two strands of DNA together into one

double helix molecule. !9. Each combination of three nucleotides on messenger RNA specifies a specific amino acid that is to be

placed in the polypeptide chain. !10. The RNA that carries amino acids to the ribosomes is a single strand of RNA that loops back on itself. !11. As a ribosome moves along a strand of messenger RNA, each codon is paired with its three nucleotides on

transfer RNA that are complementary to the three nucleotides on messenger RNA. !Part III: Short Answer 12. As a scientist, you locate the following DNA sequence. !DNA Sequence: TACTTCGCGGAA… !a.) What will be the corresponding mRNA sequence? !!b.) What amino acid sequence would be expected to form from this mRNA? !!

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c.) Imagine that a mutation caused the second amino acid to instead be Asparagine (Asn). (All other amino acids remained the same.) What kind of mutation do you hypothesize to be involved here? Why? Where exactly in the DNA sequence do you think the mutation occurred? d.) Imagine that a different mutation (of the original mRNA sequence written in part b) caused the second amino acid to instead be Glutamine (Gln), the third to instead be Alanine (Ala), and the fourth to instead be Proline (Pro). What kind of mutation do you hypothesize to be involved here? Why? Where exactly in the DNA sequence do you think the mutation occurred? Part IV: Matching 13. Match each description below to the correct nucleic acid molecule(s). (Answers may be re-used.

Some questions will have more than one correct answer.)

_____ A stable molecule that stores genetic information. Remains protected in the nucleus. _____ Along with proteins, this molecule is used to build ribosomes.

_____ This “messenger” molecule brings a copy of a gene to the ribosome. _____ This molecule is made during transcription.

_____ The monomers of this molecule are nucleotides. _____ A mutation in this molecule may be passed on to offspring.

_____ A mutation in this molecule may result in production of a non-functional protein. _____ A single-stranded nucleic acid.

_____ A nucleic acid in which complementary base pairing occurs. _____ This molecule contains the sugar deoxyribose.

_____ Nitrogenous bases include cytosine and uracil.

14. Match the descriptions below to the correct processing or modification event. (Answers may be re-used. Some questions will have more than one correct answer.)

_____ Modification made to mRNA before it leaves the nucleus; protects mRNA molecule from being broken down by enzymes.

_____ The first few amino acids in the polypeptide act as a message, telling the cell where the protein should be delivered.

_____ One primary transcript (pre-mRNA) can be used to make multiple different proteins.

_____ Chaperone proteins assist with this as a polypeptide is being built. _____ Expression of a gene is increased because more copies of its protein

product accumulate in the cell.

a.##mRNA#b.#tRNA#c.#rRNA#d.#DNA#

a. alternate#splicing#b. poly7A#tail#c. 5’#cap#(methyl#

guanine)#d. protein#folding#e. 5’#signal#sequence#f. life7span#of#mRNA#

molecule#g. life7span#of#

protein#molecule##


Gene Expression Summary:

! !Label each letter in the diagram with the following terms:!

• anticodon • mRNA • polypeptide • codon • amino acid • ribosome • tRNA

!

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name: block: date: unit 4: cell development and...

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