Wed and Thuraday 10-21 and 10-22

In Class:
Journal
Took notes on muscle tissue and Nervous tissue

Completed the muscle tissue and nerve tissue portion of the microscope lab

HW:
Finish the muscle and nerve coloring packet you got today
Study for the CH 1 test you are having next class!

Final Exam Grades

What you see on faweb right now is your total number of questions answered correctly out of 164.

I will not know the curve until Friday morning after period three takes the test.

At that point I will adjust the curve and add the 5% points to the students who tood the final exam!

See me with questions!

finalized room and times for essay make up

If you are interested in taking the essay to add some points to your ch 16-17 exam, here are the two options.

You will only be given one half hour to compete the two essays.

Thursday: Room 102 with Ms. Jager from 12-12:30

Friday: Room 123 with Mrs. Jenkins from 9:45-10:15

Opportunity to add 10 points to your ch 16-17 exam!!!

Dear Honors biology classes:

As many of you know, I had some very respectful and mature students come after school today and talk to me about the last exam. It is because of them, and how wonderfully they handled themselves that I am offering this opportunity. My hope in doing this is that it indirectly encourages all of you to advocate for what you believe in during your future endeavors in an equally mature and respectful manner.
You will each have the opportunity to earn 10 points (not to exceed 100%) onto your chapter 16-17 exam score by answering 2 essay questions. One will be on DNA replication, the other Gene expression.

This opportunity will be offered on two different dates; hopefully one of them will be convenient for you.

The first date is Thursday 6/11. It will take place after school during the make-up exam. I will post a room number tomorrow once I find the location/time of the make-up exams.

The second date will be on Friday 6/13 and will happen RIGHT after the last final in room 123.

Please be advised these essays will be graded on the facts you can provide to ensure me you have mastered the material that is often deemed, “the central dogma” to biology!

See me, or email me if you have any questions.

Good luck on your finals!

A lot of important info

Dates:
Final version of debate papers due 6/8...that is an "A" day so don't leave yours at home

I will be checking your final exam review journals on this day as well...

Final:
Bring the following to the final exam:
pencil
textbook
water

The final has a lot of questions on it. Students will only be given one and a half hours to complete. You can come early to get your book checked in so we can start right at the starting bell. Please work on your study guides as this will enable you to answer the questions faster and hence earn more points. The final's curve will be out of whoever answers the most questions correctly.

Final exam study guide

Note sure how well my study guide's formatt will translate (no punn intended) onto this blog but here goes...


Chapter 9 Cellular Respiration
1. Glycolysis (net) yields about ____ ATP and ETS yields ______.
2. Which process produces both NADH and FADH2?
3 Which process produces alcohol or lactate?
4. Which process reduces molecular oxygen to water?
5. One turn of the Krebs cycle produces
6. This is a thinker question: A young relative of yours has never had much energy. He goes to a doctor for help and is sent to the hospital for some tests. There they discover his mitochondria can use only fatty acids and amino acids for respiration, and his cells produce more lactate than normal. Of the following, which is the best explanation of his condition?
7. Inside an active mitochondrion, most electrons follow which general pathway?
8) The final electron acceptor of the electron transport chain is
9) Which metabolic pathway is common to both fermentation and cellular respiration?
10) The reducing agent in alcohol fermentation is:
11) Which of the following statements is (are) correct about an oxidation-reduction (or redox) reaction?
12. Which of the following statements describes the results of this reaction? Think oxidation/reduction

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + Energy

13. Which of the following statements about NAD+ is false?
14. Starting with one molecule of glucose, the "net" products of glycolysis are
15. Starting with citrate, how many of the following would be produced with three turns of the citric acid cycle?
16. Carbon dioxide (CO2) is released during which of the following stages of cellular respiration?
17. Cellular respiration harvests the most chemical energy from which of the following?
18. During oxidative phosphorylation, H2O is formed. Where does the oxygen for the synthesis of the water come from?
19. During aerobic cellular respiration, a proton gradient in mitochondria is generated by ________ and used primarily for ________.
20. Which process could be compared to how rushing steam turns a water wheel?
21. Assume a mitochondrion contains 58 NADH and 19 FADH2. If each of these 77 dinucleotides were used, approximately how many ATP molecules could be generated as a result of oxidative phosphorylation (chemiosmosis)?

Chapter 12: The Cell Cycle…the following questions pertain to the CELL CYCLE NOT Meiosis!
22) If there are 10 sets of sister chromatids in a cell, how many centromeres are there?

Use the following information to answer the questions below.

The lettered circles in Figure 12.1 show a diploid nucleus with four chromosomes. There are two pairs of homologous chromosomes, one long and the other short. One haploid set is symbolized as black and the other haploid set is gray. The chromosomes in the unlettered circle have not yet replicated (this is the 2n number). Choose the correct chromosomal conditions for the following stages. Note not all options are used.


Figure 12.1



25) A cell containing 92 individual chromosomes (or 46 sister chromatid sets) at metaphase of mitosis would produce two nuclei containing how many chromosomes at its completion?
26) If there are 20 centromeres in a cell at anaphase, how many chromosomes are there in each daughter cell at the end of the cell cycle?
27) Which of the following organisms does not reproduce cells by the cell cycle?
28) The correct sequence of steps on the M phase of the cell cycle is
29) What kind of nuclear division does a somatic cell undergo?
30) Which of the following are primarily responsible for cytokinesis in plant cells?

The questions below consist of five phrases or sentences concerned with the cell cycle. For each one, select the answer below that is most closely related to it. Each answer may be used once, more than once, or not at all.

A. G0
B. G1
C. S
D. G2
E. M (mitosis)

33) The MPF protein complex turns itself off by
34) A particular cyclin called “cyclin E” forms a complex with a cyclin-dependent kinase called “Cdk 2” (so these are just two different types of cyclins and Cdk’s). This complex is important for the progression of the cell from G1 into the S phase of the cell cycle. Which of the following statements is correct?
35) Which of the following is the purpose of a polar body? 36) At which stage of mitosis are chromosomes photographed in the preparation of a karyotype? HINT it is best to karyotype chromosomes once they are fully condensed 37) If the somatic liver cells of an animal have 24 chromosomes, how many chromosomes do its sperm cells have? Chapter 12 and 13 mitosis and meiosis questions

38) Which of the following is true of a species that has a chromosome number of 2n = 16? 39) When does the synaptonemal complex disappear? 40) What is the end result of the process of meiosis I and II? The following questions refer to the essential steps in meiosis described below. You will be asked to answer questions based on the numbered statements below…..
1. formation of four new nuclei, each with half the chromosomes present in the parental nucleus 2. alignment of tetrads at the metaphase plate 3. separation of sister chromatids 4. separation of the homologues; no uncoupling of the centromere 5. synapsis; chromosomes moving to the middle of the cell in pairs
43) Which of the following occurs in meiosis but not in mitosis?
44) Independent assortment is mostly affected by
45) Which of the following statements about crossing over is incorrect?
46) What name is given to the process that restores the diploid number of chromosomes present in gametes?
47) Homologous chromosomes migrate to opposite poles during ______________ of meiosis
48) A human cell containing 22 different autosomes and one Y chromosome is
49) Meiosis II is similar to mitosis in that
50. To what does the term chiasmata refer?
51. At which stage of meiosis is each chromosome composed of a single chromatid?
52. Interkinesis is different from interphase in which way?
53. Why do polar bodies form?
Matching: Match the correct definition to the correct vocabulary word
54. Anchorage Dependence
55. Density-Dependent Inhibition
56. Growth Factor (MPF Molecule)
57. Metastasis
58. Tumor
59. Cancer Cells
60. Tumor suppressing genes
Chapter 14 and 15
61. In a Mendelian monohybrid cross, which generation is always completely heterozygous?
62. In a Mendelian monohybrid cross, which generation is always completely homozygous?
63. In 1940, two researchers named Weiner and Landsteiner discovered that about 85 percent of the human population sampled possessed a blood cell protein that had been previously detected in Rhesus monkeys. This blood type was labeled Rh positive, and Rh+ was found to be dominant over the absence of the blood factor (Rh ). Under normal Mendelian inheritance, which of the following statements is FALSE?
64. Since each child of two heterozygous parents has a 1/4 chance of receiving a recessive trait from each parent,
65. In which kind of cross would you expect to find a ratio of 9:3:3:1 among the F2 offspring?
66. A testcross involves an individual exhibiting the dominant phenotype but an unknown genotype being crossed with an individual that has a(n) ___________ genotype.
67. If a human who is a tongue roller (T) and has unattached ear lobes (E) marries a person who cannot roll their tongue and has attached earlobes, could they produce an offspring that was also a non-tongue roller with attached earlobes? What would be the genotype of the first parent? The second parent?
68. Of the following which is not an autosomal dominant disorder?
69. A classical example of incomplete dominance is
70. A classical example of epistasis is
71. A classical example of multiple alleles is
72. Which of the following is a disorder in which the person has a mucus build up in their lungs? Hint, it is autosomal recessive)
73. Which type of inheritance results in continuous variation often a bell-shaped curve–because genes at many loci are involved?
74. Which disease results in deformed red blood cells, poor circulation, and anemia?
75. When crossing a homozygous recessive with a heterozygote, what is the chance of getting an offspring with the homozygous recessive phenotype?
76. Black fur in mice (B) is dominant to brown fur (b). Short tails (T) are dominant to long tails (t). What fraction of the progeny (offspring) of the cross BbTt × BBtt will have black fur and long tails?
77. A couple has three children, all of whom have brown eyes and blond hair. Both parents are homozygous for brown eyes (BB), but one is a blond (rr) and the other is a redhead (Rr). What is the probability that their next child will be a brown-eyed redhead?
78. In a cross AaBbCc × AaBbCc, what is the probability of producing the genotype (don’t get tricked by this question, I am asking for a genotype NOT a phenotype) AABBCC?
79. A woman who has blood type A, has a daughter who is type O and a son who is type B. Which of the following is a possible genotype for the son?
80. A woman has six sons. The chance that her next child will be a daughter is (Don’t let this one trick you! Remember the laws of probability. If you flip a coin 3 times and got all heads, what is the chance you will get tails on the next flip?)
81. A human male has ____ chromosomes with ____ sex chromosomes.
82. Which statement is NOT true about X linked characteristics?
83. Which of these terms would be equivalent to 3n chromosomes? Remember, this is not n+1…………..
84. Which refers to turning a chromosome segment around 180º and rejoining it to the original chromosome?
85. Karyotyping alone, can be used to diagnose which of the following genetic disorders?
86. When homologous chromosomes fail to separate during meiosis, this is termed
87. Which sex chromosome anomaly is correctly associated with the proper genotype?
88. If a woman is a carrier for the color-blind recessive allele and her husband is normal, what are their chances that a son will be color-blind?
89. In humans, X-linked diseases include all of the following EXCEPT

Decide whether the following statements apply to amniocentesis “A” or chorionic Villa Sampling “B”

Chapter 16 and 17
95) Cytosine makes up 38% of the nucleotides in a sample of DNA. Approximately, what percentage of the nucleotides in this sample will be thymine? 96) The DNA double helix has a uniform diameter because ________, which have two rings, always pair with ________, which have one ring. 97) Which of the following statements does not apply to the current model of DNA’s structure? 98) What determines the nucleotide sequence of the daughter strand that is made during DNA replication? 99) What is the function/role of both DNA polymerase I and III? In other words, what do they have in common?
Refer to the following list of enzymes to answer the following questions. The answers may be used once, more than once, or not at all.
A. helicase B. nuclease C. ligase D. DNA polymerase I E. primase
105) The Y-shaped region where the DNA double helix is actively unwound during DNA replication is called the
106) What kind of molecule or substance is the primer that is used to initiate the synthesis of a new DNA strand? 107) What is the function of topoisomerase?
108) What is one of the roles of DNA ligase in the elongation of the lagging strands during DNA replication? 109) Which of the following statements about telomeres is correct? 110) In the orientation of a nucleotide, the nitrogenous base is attached to the sugar's ________ carbon and the phosphate group is attached to the sugar's ________ carbon. 111) A biochemist isolates and purifies various molecules/enzymes needed for DNA replication. When she adds some DNA, replication occurs, but each DNA consists of a normal DNA strand paired with numerous segments of DNA. What has she probably left out of the mixture?
112) Synthesis of a new DNA strand usually begins with the addition of
113. The polypeptide making organelles residing in the cytoplasm are called
114. Amino acids are transported to the ribosome for use in building the polypeptide by
115. The process in which a RNA polymerase molecule assembles an mRNA molecule whose nucleotide sequence is complementary to the DNA sequence is called
116. Which of the following pairs with adenine in RNA?
117. The nucleotide sequence of a mRNA codon is composed of how many bases?
118. Ribosomes are complex arrangements of
119. The sites A, P, and E are progressively occupied by amino acids being assembled into a chain in protein synthesis. These sites are part of
120. Each amino acid has a specific tRNA molecule that can transport it to the site of protein synthesis. Therefore, in humans the number of different tRNA molecules would be roughly
121. In eukaryotic cells, mRNA is made as a copy of the DNA coding information in the
122. The enzyme that initiates transcription once all other things are in place is
123. The tRNA nucleotide sequence that lines up on the mRNA is called
124. Ribosome movement on the mRNA transcript is called
125. The bond that forms between the newly added amino acid and the previous amino acid on the chain is called a
126. The initiation complex for protein synthesis contains all of the following except
127. The location of protein synthesis in eukaryotic cells is the
128 The site from where the empty RNA molecules exit the ribosome is the
129 The Central Dogma of biology or gene expression is stated as
130. Which of the following answers best identifies the types of RNA associated with ribosomes during protein synthesis?
131) If the triplet CCC codes for the amino acid proline in bacteria, then in plants CCC should code for 132) Which of the following is not a part of the eukaryotic transcription initiation complex?
133) Which of the following is least related to the other items? 134. If the DNA triplet code were 3’ATG-CGT 5’, the tRNA anticodons would be
135) What is a ribozyme? 136) A mutation in which of the following parts of a gene is likely to be most damaging to a cell’s protein production? 137) Which of the following is (are) true of snRNPs?
138) Accuracy in the translation of mRNA into the primary protein depends on specificity in the….
139) Suppose the following DNA sequence was mutated from 3' AGAGAGAGAGAGAGAGAG 5' to 3' AGAAGAGAGATCGAGAGA 5'. What amino acid sequence will be generated based on this mutated DNA? 140) As a ribosome translocates along an mRNA molecule by one codon, which of the following occurs?
141. RNA splicing in eukaryotic cell protein synthesis means
A. that the product of translation, called the primary transcript is cut and put back together to produce the mature mRNA transcript
B. that the product of transcription, called the secondary transcript is cut and put back together to produce the mature tRNA transcript
C. that the product of translation, called the primary transcript is cut and put back together to produce the mature tRNA transcript
D. that the product of transcription, called the primary transcript is cut and put back together to produce the mature mRNA transcript
E. All of the above
142) The nitrogenous base adenine is found in all members of which group? 143) Which of the following does not occur during the termination phase of translation? 144) What are polyribosomes?
145) What is the effect of a nonsense mutation in a gene?
146) A possible sequence of nucleotides in the template strand of DNA that would code for the polypeptide sequence phe-leu-ile-val would be 147) What amino acid sequence will be generated, based on the following mRNA codon sequence? What is the sequence of a peptide based on the mRNA sequence 5' UUUUCUUAUUGUCUU 3'
148. RNA polymerase and DNA polymerase differ in that
149. All of the following are directly involved in translation except
150. A particular triplet of bases in the coding sequence of DNA is 3’AAA 5’. The anticodon on the tRNA that binds the mRNA codon is
151. What type of bonding is responsible for maintaining the shape of the tRNA molecule that causes it to fold among itself making that “clover” looking shape?
153. Choose the answer that has these events of protein synthesis in the proper sequence.
1. An aminoacyl-tRNA binds to the A site. 2. A peptide bond forms between the new amino acid and a polypeptide chain. 3. tRNA leaves the P site, and the P site remains vacant. 4. A small ribosomal subunit binds with mRNA. 5. tRNA translocates to the P site.

Matching: Match the scientist to the following phrases below. Options may be used once, more than once or not at all.
a. Griffith
b. Hershey and Chase
c. Chargaff’s
d. Franklin,Watson and Crick:
e. Meselson and Stahl
Matching: Match the following types of mutations to the definitions below. Note, options may be used once, more than once or not at all.

a. Point mutation
b. Base-pair substitution
c. Missense mutation
d. Nonsense mutation
e. Frameshift mutation
Ab. Insertion
Ac. Deletion
Ad. Mutagens

Wed and THurd. 5/28 and 5/29

Collected your debate papers
Took the ch 16-17 exam

Chapter 16-17 journals

NEW CHAPTERChapter 16 Journal 1
1. Please describe the structure of a nucleotide
2. What kind of polymers do nucleotide monomers make that are composed of thymine?

Chapter 16 Journal 2
1) Be able to verbally explain what a bacteriophage is and why it was it a good choice to use based on what Hershey and Chase were trying to prove...will watch animation to summarize.
2) Be able to verbally explain Meselson and Stahl’s experiment and what it proved…will watch animation to summarize.

Chapter 16 Journal 3
1) Explain some patterns you tend to notice when DNA replicates…example…if the top strand is leading the bottom is lagging…
2) Which enzyme would you classify as the most important enzyme involved in DNA replication and why?

Chapter 16-17 Journal 4

1) Read the opening paragraph on page 314…what does it mean to say…redundancy but no ambiguity?
2) Compare and contrast RNA Polymerase II and DNA polymerase III…read top paragraph on page 315
3) What is a transcription initiation complex…use image 17.8 to help…




Chapter 16-17 Journal 5
1) If you wanted to code for the following amino acids sequence, draw out what your DNA template strand would look like:
Met-Lys-Arg-Ser
Keep in mind:
• you read your DNA template strand 3’5’
• you read the RNA to code for the AA NOT the DNA
• You read RNA 5’3’ to code for AA’s




Ch 16-17 Journal 6
1. RNA polymerase moves along the template strand of DNA in the ________ direction, and adds nucleotides to the ________ end of the growing transcript. A) 3' to 5'; 5' B) 3' to 5'; 3' C) 5' to 3'; 5' D) 5' to 3'; 3'
2. During splicing, which molecular component of the spliceosome starts the excision(cutting) reaction? A) RNA B) DNA C) protein D) lipid E) sugar





Ch 16-17 Journal 7
1. Please list the 3 steps of translation
2. Please list the 3 steps within elongation of translation and explain BRIEFLY what happens in each step!


Ch 16-17 Journal 8
Each of the following is a modification of the sentence
THE CAT ATE THE RAT.
A. THE RAT ATE THE CAT B. THE TAC ATE THE RAT C. THE CAT ARE THE RAT D. THE CAT ATT HER AT E. CAT ATE THE RAT
1. Which of the above is analogous to a frameshift mutation?
2. Which of the above is analogous to a single substitution mutation?
3. A frameshift mutation could result from A) a base insertion only. B) a base deletion only. C) a base substitution only. D) deletion of three consecutive bases. E) either an insertion or a deletion of a base

4.Explain a silent mutation!




5.A biochemist isolates and purifies various molecules/enzymes needed for DNA replication. When she adds some DNA, replication occurs, but each DNA consists of a normal DNA strand paired with numerous segments of DNA. What has she probably left out of the mixture? A) DNA polymerase B) DNA ligase C) nucleotides D) Okazaki fragments E) primase

Ch 16-17 Journal 9 Only period 6 will have journal 9
Journals will be collected next class! Make sure they are organized!
1. What type of bonding is responsible for maintaining the shape of the tRNA molecule that causes it to fold among itself making that “clover” looking shape? A) covalent bonding between sulfur atoms B) ionic bonding between phosphates C) hydrogen bonding between base pairs D) van der Waals interactions between hydrogen atoms E) peptide bonding between amino acids
2. Choose the answer that has these events of protein synthesis in the proper sequence.

1. An aminoacyl-tRNA binds to the A site. 2. A peptide bond forms between the new amino acid and a polypeptide chain. 3. tRNA leaves the P site, and the P site remains vacant. 4. A small ribosomal subunit binds with mRNA. 5. tRNA translocates to the P site.
3. A) 1, 3, 2, 4, 5 B) 4, 1, 2, 5, 3 C) 5, 4, 3, 2, 1 D) 4, 1, 3, 2, 5 E) 2, 4, 5, 1, 3
4. Suppose the following DNA sequence was mutated from 3' AGAGAGAGAGAGAGAGAG 5' to 3' AGAAGAGAGATCGAGAGA 5'. What amino acid sequence will be generated based on this mutated DNA? A) arg-glu-arg-glu-arg-glu B) glu-arg-glu-leu-leu-leu C) ser-leu-ser-leu-ser-leu D) ser-ser-leu E) leu-phe-arg-glu-glu-glu

4) A mutant bacterial cell has a defective aminoacyl synthetase that attaches a lysine to tRNAs with the anticodon AAA instead of a phenylalanine. The consequence of this for the cell will be that A) none of the proteins in the cell will contain phenylalanine. B) proteins in the cell will include lysine instead of phenylalanine at amino acid positions specified by the codon UUU. C) the cell will compensate for the defect by attaching phenylalanine to tRNAs with lysine-specifying anticodons. D) the ribosome will skip a codon every time a UUU is encountered. E) None of the above will occur; the cell will recognize the error and destroy the tRNA.

5-26 and 5-27 HBio period 2,3,6

Watched a stem cell debate
Passed out and explaind your debate HW

HW: Study for your test you are having next class on ch 16-17

Be sure to complete your first draft of your debate paper...due next class which is the day of your test

Get journals ready to be checked next class!

Hbio Period 5/21 and 5/22

journal
collected HW packets
answers to HW packets
Went over the notes for ch 17...fast as you should have had them printed out ahead of time

Rest of class was used to finish the projects

Dates for Period 2+3
exam 5/28
Projects due 6/1
Stem cell debate in class 6/1
Final draft of stem cell papers due 6/8
First draft of stem cell papers due 5/28

Dates for Period 6
exam 5/29
Projects due 6/2
Stem cell debate in class 6/2
Final draft of stem cell papers due 6/8
First draft of stem cell papers due 5/29

Hbio Period 6 5/20/09

journal
notes on translation
more project time

Print out notes for next class....blog entry titled: Vocab for ch 17 notes
HW packets due next class

You will get your debate assignement next class as well!

Date Changes:
ch 16/17 test-friday 5/29
ch 16/17 projects due 6/2

Helpful Ch 17 Animations

Helpful animations for translation and transcription

Link for all stages of gene expression
http://www.exrx.net/Lists/Directory.html

transcription website
http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swf


RNA Processing Website
http://highered.mcgraw-hill.com/olc/dl/120077/bio30.swf
http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter15/animations.html#


translation website
http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translation.swf
http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter15/animations.html#


Compare Proks/Euks transcription
http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter15/animations.html#

http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter15/animations.html#

Monday Period 6... 5-18

journals
review of transcrioption from last class...felt you all needed more clarification
started the transcripton portion of your projects

HW:
see new dates on prior blog
keep working on your HW packets

NEW DUES DATES

Hey all:
Here are some new dates, sorry they have changed AGAIN!

period 2/3
5/21 HW packets due
5/26 Ch. 16-17 exam
6/1 stem cell debate day

period 6
5/22 HW packets due
5/27ch 16-17 exam
6/2 debate on stem cells

Vocab for ch 17 notes

Ch 17: DNA RNA  Protein

Transcription: direction known as down Stream and reads DNA  RNA

mRNA: Takes DNA code out of nucleus into cytoplasm for translation

Translation: turning mRNA  proteins

Ribosomes: large and small subunits that make proteins

RNA Processing: editing the pre mRNA before it leaves the nucleus, adding tail, rid introns

Primary Transcript: The pre mRNA before processing

Triplet Code: three bases on the RNA that code for one AA…..see page 314

Template DNA Strand: read 3’ 5’ to make RNA 5’3’

Codons: 5’3’ on RNA and non-template DNA strand = 3 nucleotides that code for protein

RNA Polymerase (II Euks): Opens DNA and brings in RNA nucleotides
5-3’ Rule
No need for primer

Promoter: Specific starting gene sequence on DNA

Terminator: Stopping point

Stages of Transcription: Initiation, elongation, termination








Initiation: Getting ready to start transcription
 Transcription Unit: Area between Promoter and Terminator that gets transcribed
 Transcription Factors: Proteins that doc onto promoter and signal RNA Polymerase to bind to DNA in Euks
 Transcription Initiation Complex
Transcription factors
RNA Polymerase II
Promoter

TATA box: Area where transcription factors bind on DNA so RNA Polymerase can doc…lots of T,A’s

Elongation: Making the RNA Strand

Termination: Reaching a stop point and ceasing RNA formation.

Area where Transcription factors fall off 10-35 nucleotides downstream from polyadenylation signal (AAUAAA)….not fully understood in EUKS

RNA Processing:
Pre mRNA Modification

5’ Cap: made during transcription composed of modified G nucleotide with three phosphates

3’ Tail: Poly-A Tail: Made at end of elongation many A nucleotides

RNA Splicing: Cut and paste job in Pre mRNA

Introns: Non-coding regions of pre mRNA that get spliced away

Exons: Coding regions of RNA that stay

Spliceosome: Collection of many snRNPs
snRNPs: (small nuclear ribonucleoproteins) recognize splicing sites composed of proteins and RNA
snRNA the RNA in a snRNP, base pair with RNA in pre mRNA to tag cut areas

Ribozymes: RNA that can function as enzymes. Base pair with self forming enzyme blobs because it is single stranded

Translation: Making a protein from mRNA

Transfer RNA: Brings AA from cytoplasm to ribosomes

Anticodon: base sequence on the tRNA that base pairs with mRNA in ribosome 3’5’

Aminoacyl-tRNA synthetase: stored in the cytoplasm and joins the correct AA to the proper tRNA, then is recycled, 20 different ones

rRNA: The type of RNA found in the structure of a ribosome

P (peptidyl tRNA) Site: Second docking Slot

A (aminoacyl tRNA) Site: First docking Slot

E (Exit) Site: Third docking Slot

APE!


Initiation:
Image 17.17
 Completes a initiation complex
o mRNA
o Initiator tRNA (met)
o Small ribosome
o Large ribosome
o All brought together by initiation complex proteins
o Used GTP as energy
o At completion Met tRNA is in P site and A site is vacant

Elongation:
Image 17.18
 Uses elongation factors to complete until STOP codon reached
 Uses GTP as energy
 Has three steps embedded within it
o Codon recognition
o Peptide bond formation
o Translocation






Termination
Image 17.19
1. Stop Codon in A site
2. Codes for a release factor
3. Causes addition of water to growing AA chain instead of an AA
4. Hydrolyzes polypeptide from P site via exit tunnel in ribosome
5. Everything else dissembles

Thursday and Friday 5/14 and 5/15 IMPORTANT DATES

In class:
journal
notes on transcription and RNA processing
started your in class projects

Dates to remember:

Period 6
5/18 ch 16 and 17 HW packets are due
5/20 ch 16 and 17 exam
5/27 ch 17 projects due
5/29 debate in class

Period 2 and 3
5/19ch 16 and 17 HW packets are due
5/21 ch 16 and 17 exam
5/28 ch 17 projects due
6/1 debate in class

Honors Bio Period

Journal
collected outlines from last class...These are due for period 6 next class!
Did a DNA isolation Lab
Started ch 17 notes
Passed out Ch 17 HW packet

NEW DATES:
ALL HW packets due 5/18 or 5/19
Ch 16-17 exam 5/20 and 5/21


Translation/transcription projects due 5/27 or 5/28

Friday 5-8 and Monday 5-11

No journal today....
assigned HW...which is to outline pages 305-307
watched stem cell lecture and answered questions

Good luck ont he AP bio exam for those of you who are taking it!

Wed and Thursday 5-6 and 5-7

journal (except for period 6 you will have two next class)
started and finished projects!

Animation links per your request!

http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/dna-rna2.swf



http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter14/animations.html#



http://www.bioteach.ubc.ca/TeachingResources/MolecularBiology/DNAReplication.swf

Monday and Tuesday 5/4 and 5/5

journal/showed animations
notes on DNA replication
showed some DNA replication animations
started your DNA replication class projects!

Jenkins on a field trip Wed 5/6!!!!!!!!!

Vocabulary Quiz for Mon and Tues Canceled

for those of you who checked the blog...you can mark off studying for your quiz on tonight's agenda!

NO quiz next class!

Hbio Thursday and Friday April 30th and May 1st

Journal
Notes...
quiz next class on

•DNA structre
•DNA replication vocabulary words…posted on blog!

DNA Replication Vocabulary see below

Helicase unwinding breaks H bonds (green)

Single Strand Binding Protein stabilizer

DNA Polymerase III adds DNA to primer (orange)

Primase RNA primer (pink)

DNA Polymerase I replaces primer (yellow)

DNA Ligase Glues 5’ and 3’ ends (turquoise)

Topoisomerase corrects over-winding

Origin of Replication where synthesis starts

Leading Strand works towards the replication fork

Lagging Strand works away from the replication fork

Okazaki Fragments lagging strand fragments

Telomers base buffers

Telomerase enzymes that add telomers in germ cells to cancer cells

Parent Strand The strand of DNA that serves as a template to make the “phantom” strand (dark black)

Daughter Strand The strand we are trying to make by using the original DNA template (light blue)

Mismatch pair: incorrect base pairing

Proofreading: done by DNA Polymerase III which removes or adds bases as needed

Nuclease: cuts out the mismatch pair

Nucleotide excision repair: uses ligase and DNA polymerase to fix a mismatch
Polymerase fills gaps
Ligase fuses gaps

friday and monday 4-23 and 4-26

journal
short lecture on diseases
practice genetics worksheet that was turned in for credit

Test next class
Be sure to bring Journals..there are nine total!

Bio Test Delayed

Because of the math final the test for ch 14-15 will occur on:

Period 2+3 = 4-29
Period 6 = 4-28

All other dates remain the same such as when hw packets are due etc.

Wed and Thurs. 4-22 and 4-23 Hbio Period 2,3,6

Journal
Collected HW Packets
Answers to HW packet
Misc. notes
If time, another genetics practice worksheet

Ch 14-15 Exam Next Class

Journals due next class, just a reminder I am only collecting journals that are labeled as "journal 1," "Journals 2, " etc. See prior posting for any journals you may have missed!

NEW JOURNAL…..NEW RULES!!!!!!!!!!
For FULL credit journals MUST be labeled by journal entry!

Journal 1 Chap 14/15
Read page 252 and provide some “facts” about who Mendel was!

Journal 2 Chap 14/15
1) Cross a homozygous dominant tall plant with a heterozygous tall plant and anaylyze the genotypical outcomes of the F1 generation…phenotypical….
2) Which of the following are genotypes and which are gametes?
a. AA
b. A
c. Bb
d. BB
e. C

Journal 3 Chap 14/15
1. BbDD (B brown, D deaf) is mated to one with BBdd. What is the chance of obtaining an offspring that is
a. Brown/NOT deaf?
b. Brown/deaf?
2. When you are done with this journal finish your ws from last class…we are going to have an overhead of notes in just a sec!

Journal 4 Chap 14/15
Do overhead practice problem set 11.5

Journal 5 Chapter 14/15
Considering incomplete dominance and the following key answer the following question.
TA = tall
TB = short
PR = purple
PQ = white

Parents = TATBPRPQ x TATAPRPR

1. What are the chances of having a medium/lilac flower?

Journal 6 Chapter 14/15
gene
allele
principle of segregation
principle of independent assortment

different forms of a gene for the same trait

The law that states the different forms of two alleles (homologous chromosomes) will separate independently of each other into different gametes

a segment/piece of DNA that codes for a trait

This law states that factors for different characters (on different chromosomes) separate independently of each other. This is why you have to consider EVERY possible combination that can occur when you are tracking a dihybrid cross

Journal 7 Chapter 14/15
1. Using pages 265-268 make a list of all the autosomal dominant and a list of the autosomal recessive inherited disorders and provide a brief explanation of each.
2. Note to self, please be sure to read and understand pages section 15.4 of your book. We may not be going over this in class but it will be on the test! Show PPT on this from notes!
3. Today Jenkins will show you some examples of sex chromos altered

Journal 8 Chapter 14/15

Make sure your journals are in order for next class when they will be checked off

Make sure to pay attention to chromosomal # abnormalities and autosomal dom/rec and sex linked diseases info..see blog for full description

1. Explain why generally, it is not possible to determine whether nondisjunction failed to occur in oogenesis or spermatogenesis. However, it is possible to assert that xyy resulted in nondisjunction in spermatogenesis

Decide whether the following statements apply to amniocentesis “A” or chorionic Villa Sampling “B”

2. Obtains cells from the region where the placenta will develop
3. Takes a sample from the amniotic fluid from the uterus
4. Can determine more types of abnormalities. In other words, is not limited to just a disorders revealed by a karyotype
5. Of the two procedures, this test has the lowest risk of a spontaneous abortion
6. This test can be done earlier in the pregnancy

7. Decide the inheritance pattern of the following pedigrees….be ready to explain!

Journal 9 ch 14-15
Mom: Dad
homozygous hemophilia Has hemophilia
homozygous cystic fibrosis carrier of cystic fibrosis
blood type AB Homozygous for blood B
Rh- Heterozygous Rh+
Heterozygous for Huntington’s Disease Heterozygous for Huntington’s


Showing your work mathematically, please give me the phenotypical fraction among all the offspring
that will be male hemophiliacs, with cystic fibrosis, blood type BB, Rh+, with Huntington’s
disease. Yes, I know this kid was dealt a bad hand of cards!

Mon and Tues 4-20 and 4-21 HBio

Journal
Notes on pedigrees and misc items so you could finish your HW packets
pedigree worksheet that was turned it at class end

HW packets due next class
Please see below info for disease info that may be helpful for your test...some of these are in your books!


•Tay-Sachs Disease
–Progressive deterioration of psychomotor functions due to lacking hex A enzyme and the ability to store it’s lipid substrate
–Causes build up of lipids in the brain
–1:3,600 Jewish have the disorder
–Developing symptoms 4-8mths old
–Child gradually becomes blind and helpless, seizures, paralyzed
–Death by age 3 – 4 No cure


•Cystic Fibrosis
–Mucus in bronchial tubes and pancreatic ducts is particularly thick and viscous due to lack of water due to the NaCl pump not working.
–Most common lethal genetic disorders among Caucasians
–1:20 Caucasians is a carrier
–1:3,000 newborns have disorder
–Clogged pancreatic ducts do not allow digestive enzymes to reach stomach so apple sauce mixed with digestive enzymes is taken before every meal
–Die by age 37
–Have isolated gene on chromosome #7


•Phenylketonuria (PKU)
–Lack enzyme for normal metabolism of phenylalanine which effects nervous system development
•Need to change aa (phenylalanine) into another aa (tyrosine)
–Gene on Chromosome #12
–Lack enzyme needed to break down the amino acid PKU
–PKU accumulates in the urine
–Tested at birth, placed on low PKU diet until brain is developed…age 7 some for lifePregnant woman must be on low PKU diet to protect unborn baby


•Neurofibromatosis
–Tan or dark spots develop on skin and darken. Small, benign tumors may arise from fibrous nerve coverings
–Equal among all ethnic groups
–Many children with the disorder have hyperactivity and learning disabilities
–Chromosome # 17


•Huntington Disease
–Neurological disorder leading to progressive degeneration of brain cells, in turn causing severe muscle spasms and personality disorders
–1:20,000 people are affected with a mutation of the gene on chromo 4
–The huntington protein has too many copies of AA Glutamine in the protein
–Normal is 10-25 glutamines long
–Affected have a protein with 36+ glutamines
•Changes shape and forms large clumps in nervous system and causes other proteins to clump to it
–Unaffected until middle age
–There is a test, would you want to be tested?

thurs and fri 4/16 and 4/16

Journal while Jenkins checked off your worksheets
Answers to worksheets
quiz on genetics up to this point
blood lab...when you are done with the quiz...work on your HW packets if you finished early while the others finished the lab
notes on chromosomal number abnormalities

HW packets are due wed 22nd and 23rd unless otherwise stated...

Test scheduled for friday the 24th and 27th depending on what period I have you!

Tues and Wed 4/14 and 4/15

Journal
collected babies from last class that you were supposed to finish as hw
Misc. notes
Sex linked notes
Blood lab and sex linked ws

HW:
1. Study for quiz you are having next class on...
vocab
blood typing
sex linked
dihybrid
incomplete dominance
codominance
2. Finish sex linked, mult allele ws for HW...answers next class

AP Study Session Dates/Topics!
2:45-4:00 starting promtly each day! If you come in late, please come in quietly and join in on the study session!

4-15 unit four of study guide...focus on Hardy-Weinberg
4-23 Anatomy and Physiology focus on Muscles, cardiovascualr system, immune system and
misc. orginization
4-29 plants
5-7 Day for you to come in and take some of the practice exams in your study guide

Tues and Wed 47 and 4/8

journal
answers to di and mono ws
finished blood notes
did blood ws

Make sure you have started your HW packet by now!
Jenkins will be out on Thursday for a field trip!

fri and monday 4/3 and 4/6

jounrnal
notes on mult and addition law'
notes on codom/incomplete dom/blood
finished your mono and dihybrid ws in class....please finish for HW as the answers will be given next class!

wed and thursday 4/1 and 4/2 HBio

Journal
Collected your mitosis projects
Changed seats
Passed out YUMMY brownies!
did some dihybrid MATH
Started a monohybrid and dihybrid worksheet that you did not have time to finish
You will get the first 10 minutes of next class to finish the above worksheets

HBio Period 2,3,6 Monday and Tuesday 3/30 and 3/31

journals
started ch 14 notes
passed out ch 14-15 hw packets

Mitosis/meiosis projects due next class!!!!

due dates after spring break!

Hey Hbio kids!

Just a reminder your mitosis and meiosis projects are due on april 1 and april 2 depending on when you have my class!

We will be starting chapter 14-15 if you want to start reading while you are on break!

Enjoy yourselves and YA HOOO thesis is over!

The AP study packets will be in the main office for the first week after spring break!

wed and thurs 3/18 and 3/19

ch 12-13 exam
checked off your journals

NO HW!!!!!!!!! Enjoy spring break and get your thesis done!!!!!!!!

mon and tues 3/16 and 3/17

collected your Hw packets
journal
speratogenesis notes/oogenesis notes
gave hw answers but did not have enough time to finish.......

you can pick up your hw packets anytime after school monday...they are in the extras bin! I will also have some answer sheets located in that drawer for you to use....

study session at lunch tuesday as i have meetings after school tues

NEW DUE DATES!!!!!!!

Ok guys, because I like you all so much and you are so stressed about thesis........

your mitosis and meiosis projects are going to be due the first time i see you after spring break

period 2+3 due: 3/31
period 6 due: 3/30

Thursday and Friday 3/12 and 3/13

In class:
Journal
Meiosis quiz
classtime to start your meiosis projects

HW:
Finish your meiosis projects they are due two classes from now! You may get a few more minutes to work on them next class!!!
HW packets are due next class

Check past blogs to see important upcoming dates for your project due dates and ch 12-13 exam!

Tuesday and Wed 3/10 and 3/11

journal
meiosis notes
meiosis quiz practice

HW study for the quiz you are having next class...see blog for a complete list of the vocab you will need to match

Meiosis vocab words you may want to print for next class

Meiosis Vocabulary Words

ü Sex Chromosomes
ü Autosomes
ü Gametes
o Egg
o Sperm
ü Zygote
ü Meiosis I
o PI
§ Synapsis
§ Crossing over
§ Tetrad
§ chiasmata
o MI
o AI
o TI
o Cytokinesis
ü Meiosis II
o PII
o MII
o AII
o TII
o Cytokinesis
ü Genetic Variation
o Independent Assortment
o Crossing Over
o Random Fertilization
ü Oogenesis
o Oogonium
o Primary oocyte
o Secondary oocyte
o Polar body
ü Spermatogenesis
o Spermatogonium
o Primary spermatocyte
o Secondary spermatocyte
o Spermatids

Period 6 HBio Dates

Here are some tentative dates for ch 12-13

Meiosis quiz 3-13
Class time to complete your mitosis/meiosis project 3-13
ch 12-13 HW packets due 3-17
Twin presentations for SOME students 3-17
Ch 12-13 exam 3-19

Period 2-3 HBio Tentative dates

Here are some tentative dates for ch 12-13

Meiosis quiz 3-12
Class time to complete your mitosis/meiosis project 3-12
ch 12-13 HW packets due 3-16
Twin presentations for SOME students 3-16
Ch 12-13 exam 3-18

Friday and Monday 3-6 and 3-9

First 10 minutes of class to gather with your peers and organize your presentations
Heard the presentations from your peers

Wed and Thurs 3/5 and 3/6 all HBio Classes

Journal

• Time to work with your assigned group on the cancer reading
• presentations are due next class
• I suggest each student print out a copy of the cancer reading questions that are fair game for the test and bring them to class with you so you can answer them while presentations are going on
• see blog for presentaions details
• don't forget you will be turning in your vocab words and grading sheets for your group members along with a hard copy of your project

cancer reading questions

Print out and bring to class

Cancer Reading Questions

Please answer the following questions on a separate piece of paper. These questions are fair game for the test.
Please DO NOT WRITE on the cancer reading, it is just a reading to get done in class.
Feel free to talk this information over with your peers!

Questions:
How are bacterial infections and cancer infections different?
Damage Control: Tumor Suppressor Genes
What four things do normal cells have in place as a way of damage control?
What is cellular suicide called?
How is necrotic cell death different from apoptosis?
P53 is a key protein involved in detecting cellular damage, what are three of its major functions?
What happens when the gene coding for p53 is mutated?
What is the definition of a tumor suppressor gene? What are some of the jobs these genes encode proteins to do?
Why is a mutation in a tumor suppressor gene bad?
Promoting Cellular Division: oncogenes
What happens when protoncogenes become oncogenes? Give a few examples
What would happen to a cell that had an oncogene mutation and a tumor suppressor mutation?



11 What are the six hallmarks of cancer cells? Please briefly explain each!

a.
b.
c.
d.
e.
f



Evolution of Tumors:
What are some of the many changes that have to occur in the cell for it to become cancerous?
How is cancer linked to evolution?

cancer proj reqs

Cancer Jig-Sawing Presentation Rubric
Five Groups Total for each class!
1) Cancer cells have profound genetic defects-STOP at cell cycle title
2) Cell Cycle – stop at six hallmarks of cancer title
3) Six hallmarks of cancer 1-3
4) Six hallmarks of cancer 4-6
5) Evolution of tumor cells – end of packet
Below you will find the criteria for your presentation. You will be given one class period to organize your thoughts and take notes on your topic and talk with your group members. Please note, the reading packets will not be available outside of class. You are invited to stay after school/Reps if you need more time with the packet.
1) Equal participation by all members in the delivery of your topic
2) Good flow of information…presented in order it was given in the reading
3) Short, to the point notes. Remember your notes should prompt you on what you are presenting about. You should glance at them every once in a while to keep your focus while you are in front of the class or to remember big words but you should in NO WAY SHAPE OR FORM READ NOTES to the class. You really should have your material memorized when you get up to present!
4) Wordy notes will not be acceptable! Your notes can either be PPT or overhead style or BOTH like I often do. Use the PPT for images and overhead for notes!
5) An overall feeling by Mrs. Jenkins that your group has a thorough understanding of what you are presenting about
6) The ability to answer any questions your peers may have to re-clarify what you presented on! Believe me, there are a lot of unanswered questions out there about cancer and I don’t expect you to know the answers!
Notes:
1) This will count as a lab grade
2) You will receive an individual grade and a group grade
3) If anyone in your group is not prepared it will reflect on the whole “group” grade
4) Make sure any computer portions of your project work before the presentation day or your grade will be affected!
Turn into Mrs. Jenkins:
1) Any part of your presentation. If you do a PPT, please print them out and give me a HARD copy. Also please plan to turn in any overheads or other notes to me. HARD COPIES only!
2) A piece of paper with all the group members listed, including your own name. Please list your name as the first name. On that sheet of paper, please give each member a grade based on how much effort they put into their part of the project. Use the grading scale and example below:
Jenny Jenkins 3
Denise Farrell 3
Dawn Guildner 3
Katie Cave 3

1 did not collaborate well with group, was unprepared, had not idea what they were talking about, read their slides etc.
2 provided an average amount of effort, did not fully understand their material, mostly prepared but had to read a good amount of their slides
3 really worked hard, was prepared, helpful in the group understanding the material got up and rocked the presentation portion of the project

Mon and Tues 3/2 and 3/3

journal
Cancer notes
given some time to work on mitosis projects
goodies passed out for good behavior

Thursday and Friday 2/26 and 2/27 ALL HBio Classes

10 minutes of journal time
Mitosis Vocab quiz....see earlier blog for list of words you can expect to see on quiz
started your cell cycle drawing projects

You did not finish these project in class, but you will be given some more classtime in the near future to work on these...

Next class we are going to talk about cancer and you will be given a group to work with and you will create a presentaion based on a reading I assign your group!

Have a great weekend guys!

List of Vocab words your quiz will be on!

Cell Cycle Vocabulary Words

ü Cell Division
ü Cell Cycle
o Mitosis
§ Interphase
· G1
· S
· G2
§ Prophase
· Chromatin
· Chromosomes
o Histones
§ Metaphase
· Metaphase plate
§ Anaphase
· Sister chromatids
· Centromeres
§ Telophase
o Cytokinesis
· Cleavage
· Cleavage Furrow
· Cell Plate
· Binary Fission
o Origin of Replication
ü Somatic Cells
ü Karyotype
ü Homologous Chromosomes
ü Centrosome
ü Spindle Fibers
ü Asters
ü Kinetochore
ü Kinetochore Spindle Fibers
ü Nonkinetochore Spindle Fibers
ü Diploid
ü Haploid

Tuesday and Wed 2/24 and 2/25 all classes

Journal
finished the mitosis vocab notes with lots of discussion
Vacab quiz next class...will be scantron/matching

You will be starting your in class mitosis projects next class...come ready to do that!

You should be working on your HW packets! They are not due for a while but don't save all the fun for one night!

Monday 2/23/09 Hbio Period 6

Journal...teacher eval
notes on mitosis vocab...we did not finish!
15 minutes to work on lab
labs due to Mrs. Jenkins Wed 2/25
Let you look over your Chapter 9 exams....you could not keep them yet as people are making them up on Tuesday

You should be working on your HW packets!

Jenkins will be out Thurs and Fri 2/19 amd 2/20

SUB PLANS!!!!!!

When I am out you will be completing a reading on cancer and answering questions. The answers to these questions are due at the end of class! Do as much of it as you can!

Wed. 2/18 HBio Period 2 and 3

Journal
notes on mitosis vocab...we did not finish!
15 minutes to work on lab
labs due to Mrs. Jenkins tuesday 2/24
Explained sub plans for Mrs. Jenkins out for conference next class


You should be working on your HW packets!

2-13-09 Period 2+3 Hbio and 2-17-09 Period 6

Checked your ch. 9 journals
took your ch 9 test
recieved your ch 12 + 13 HW packet

for anyone who was absent for ch 9 test........see blog posting called "ch 9 test makeups!"

Period 2+3 enjoy the long weekend!

Ch 9 TEST MAKE UPS HBIO!!!!!!!

If you were absent for the day of your ch 9 test, plan to stay after school on wed 2/18 to make it up!

I am not available after school on Monday as I have an academic council meeting and I will be out of the building at a conference all day thurday and Friday!

Remember it is part of the CCHS handbook guidelines that if you are absent on the day of a test you have one school day to make that up. Please see me if you have concerns. For anyone who can not stay this day and has to take the test the following week, your exam will be all essay.

Have a great weekend!

Ch 9 Hbio journals!

Here are the Ch 9 journals......sorry for any images that did not transfer!

Start Chapter 9 Respiration Journal
Look in your book and tell me where in the cell the following reactions take place:

glycolysis
citric acid cycle
electron transport chain

for any steps that occur in the mitochondria please state where in the mitochondria





Chapter 9 Journal 2
In the following equation state the following:
C4H6O5 + NAD+ à C4H4O5 + NADH + H+

Pyruvate + NADH + H+ àLactate + NAD+
Oxidizing agent
Reducing agent
Who is oxidized
Who is reduced
Describe cell resp to a third grader and explain the over goal of cellular respiration’s sugar and O2.

Chapter 9 Journal 3

1) The molecule that functions as the reducing agent in a redox or oxidation-reduction reaction
A) gains electrons and gains energy.
B) loses electrons and loses energy.
C) gains electrons and loses energy.
D) loses electrons and gains energy.
E) neither gains nor loses electrons, but gains or loses energy.

2) When electrons move closer to a more electronegative atom, what happens?
A) Energy is released.
B) Energy is consumed.
C) The more electronegative atom is reduced.
D) The more electronegative atom is oxidized.
E) A and C are correct.




3 ) Substrate-level phosphorylation accounts for approximately what percentage of the ATP formed during glycolysis?
A) 0%
B) 2%
C) 10%
D) 38%
E) 100%

4) During glycolysis, when glucose is catabolized to pyruvate, most of the energy of glucose is
A) transferred to ADP, forming ATP.
B) transferred directly to ATP.
C) retained in the pyruvate.
D) stored in the NADH produced.
E) used to phosphorylate fructose to form fructose-6-phosphate.



Do the rest as a class

5) In which step is an inorganic phosphate added to the reactant?

6) In which reaction does an intermediate pathway become oxidized?

7) Which step involves an endergonic reaction?

8) Which step consists of a phosphorylation reaction in which ATP is the phosphate source?







Chapter 9 Journal 4
1) Which of the following statements about NAD+ is false?
A) NAD+ is reduced to NADH during both glycolysis and the citric acid cycle.
B) NAD+ has more chemical energy than NADH.
C) NAD+ is reduced by the action of dehydrogenases.
D) NAD+ can receive electrons for use in oxidative phosphorylation.
E) In the absence of NAD+, glycolysis cannot function.

2) Which of the following statements about glycolysis false?
A) Glycolysis has steps involving oxidation-reduction reactions.
B) The enzymes of glycolysis are located in the cytosol of the cell.
C) Glycolysis can operate in the complete absence of O2.
D) The end products of glycolysis are CO2 and H2O.
E) Glycolysis makes ATP exclusively through substrate-level phosphorylation.

Chapter 9 Journal 5
1. In the presence of oxygen, the three-carbon compound pyruvate can be catabolized in the citric acid cycle. First, however, the pyruvate 1) loses a carbon, which is given off as a molecule of CO2, 2) is oxidized to form a two-carbon compound called acetate, and 3) is bonded to coenzyme A. These three steps result in the formation of
A) acetyl CoA, O2, and ATP.
B) acetyl CoA, FADH2, and CO2.
C) acetyl CoA, FAD, H2, and CO2.
D) acetyl CoA, NADH, H+, and CO2.
E) acetyl CoA, NAD+, ATP, and CO2
2. During cellular respiration, acetyl CoA accumulates in which location?
l A) cytosol
l B) mitochondrial outer membrane
l C) mitochondrial inner membrane
l D) mitochondrial intermembrane space
l E) mitochondrial matrix

3 How many carbon atoms are fed into the citric acid cycle as a result of the oxidation of one molecule of pyruvate?
l A) 2
l B) 4
l C) 6
l D) 8
l E) 10
4.All of the following are functions of the citric acid cycle except
l A) production of ATP.
l B) production of NADH.
l C) production of FADH2.
l D) release of carbon dioxide.
l E) adding electrons and protons to oxygen, forming water.

Chapter 9 Journal 6
1) Cellular respiration harvests the most chemical energy from which of the following?
A) substrate-level phosphorylation
B) chemiosmotic phosphorylation
C) converting oxygen to ATP
D) transferring electrons from organic molecules to pyruvate
E) generating carbon dioxide

2) Where are the proteins of the electron transport chain located?
A) cytosol
B) mitochondrial outer membrane
C) mitochondrial inner membrane/cristae
D) mitochondrial intermembrane space
E) mitochondrial matrix

3) Inside an active mitochondrion, most electrons follow which pathway?
A) glycolysis → NADH → oxidative phosphorylation → ATP → oxygen
B) citric acid cycle → FADH2 → electron transport chain → ATP
C) electron transport chain → citric acid cycle → ATP → oxygen
D) pyruvate → citric acid cycle → ATP → NADH → oxygen
E) citric acid cycle → NADH → electron transport chain → oxygen

4) Starting with one molecule of citrate and ending with oxaloacetate, how many ATP molecules can be formed from oxidative phosphorylation (chemiosmosis)?
A) 1
B) 3
C) 4
D) 11
E) 12
Chapter 9 journal 7

1) Muscle cells in oxygen deprivation convert pyruvate to ________, and in this step gain ________.
A) lactate; ATP
B) alcohol; CO2
C) alcohol; ATP
D) ATP; NADH2
E) lactate; NAD+








2) An organism is discovered that consumes a considerable amount of sugar, yet does not gain much weight when denied air. Curiously, the consumption of sugar increases as air is removed from the organism's environment, but the organism seems to thrive even in the absence of air. When returned to normal air, the organism does fine. Which of the following best describes the organism?
A) It must use a molecule other than oxygen to accept electrons from the electron transport chain.
B) It is a normal eukaryotic organism.
C) The organism obviously lacks the citric acid cycle and electron transport chain.
D) It is an anaerobic organism.
E) It is a facultative anaerobe.







3) Why is glycolysis considered to be one of the first metabolic pathways to have evolved?
A) It produces much less ATP than does oxidative phosphorylation.
B) It is found in the cytosol, does not involve oxygen, and is present in most organisms.
C) It is found in prokaryotic cells but not in eukaryotic cells.
D) It relies on chemiosmosis which is a metabolic mechanism present only in the first cells-prokaryotic cells.
E) It requires the presence of membrane-enclosed cell organelles found only in eukaryotic cells.










Chapter 9 Journal 8
1) Why would an organism utilize fermentation if it was wasteful of the energy in food molecules and posed the threat of killing itself with high levels of toxic alcohol?
A. The organism can survive short spells of anaerobic conditions and maintain growth and reproduction.
B. If glucose levels are not high, there may be time to scatter the alcohol “waste.”
C. Fermentation can provide a rapid burst of ATP since it does not have to go through the full breakdown cycle.
D. All of the above are advantages.
E. None of the above is an advantage; anaerobes only survive where aerobes cannot.





2) The primary role of oxygen in cellular respiration is to
A) yield energy in the form of ATP as it is passed down the respiratory chain.
B) act as an acceptor for electrons and hydrogen, forming water.
C) combine with carbon, forming CO2.
D) combine with lactate, forming pyruvate.
E) catalyze the reactions of glycolysis.

3) Which of these pairs of processes are anaerobic?
A. fermentation and glycolysis
B. fermentation and the Krebs cycle
C. glycolysis and the Krebs cycle
D. the Krebs cycle and the electron transport system
E. glycolysis and the electron transport system

2-12-09 Hbio Period 6

Collected class packets while you did your journals
went over the answers to the class packets
talked about how proteins and fats enter cell respiration
talked about the lab and interpreted the data
Answered the lab questions and graphed the required data with your lab group

HW: Study for test that is next class on Tuesday the 17th!!!!!!

2/10 Period 2 and 3 Hbio

Collected class packets while you did your journals

went over the answers to the class packets

talked about how proteins and fats enter cell respiration

talked about the lab and interpreted the data

Answered the lab questions and graphed the required data with your lab group which was due at the end of class

HW: Study for test that is next class on Friday the 13th YIKES!!!!!!!!!

2/9 Period 6 HBio

YIKES! Only 20 minutes of class so for those of you who were here....12 of you........you got fat pellets and an assignment to complete for extra credit!

Class packets are due next class.........THURSDAY!!!!!!!!!!

Thursday/Friday 2/5 and 2/6 BHio Periods 2,3,6

In Class
Journal
Explained respiration lab
conducted respiration lab and worked on class packets during down time

HW:
Finish class packets for HW...you should not have more than an hour of work to do on this if you have been getting small amounts done in class over the last 3 weeks. It will be collected at the start of next class which is when you will finish the lab questions/graphs!

2-3-09 and 2-4-09 all HBio Classes

Journal
finished lecture on chapter 9
finished class packet in class
Will go over answers at the start of next class

HW
Read the lab on cellular respiration I will check that you have made notes on the procedures at the start of next class
Finish class packets if necessary

Ch 9 exams are tentatively as follows
P6 Monday 2/9/09
P2+3 Tuesday 2/10/09

1-30-09 Hbio Period 6 and 2-2-09 P 2+3

Journal
Notes on ETS and chemiosmosis...took longer than expected!
Heard a GREAT SONG!!!!!!

NO HW

Have a great weekend!

HBio P6 1-28-09 AND Period 2/3 1-29-09

Happy Second Semester!!!!

Journal
Changed seats
Assigned new duties
gave you 15 minutes to look at your final
Notes on krebs cycle and transition reactions

Class packet 9.7, multiple choice 10 and bookwork 9.3

HW: Read about ETS and Chemiosmosis

ALL HONORS BIO FINAL INFO PERIOD 2,3,6

Instead of having an essay on your final exam, you will be turning in your study guide for 5 points on the final. If only half of your study guide is filled out you will only receive half the points.

Please bring your completed study guide to the final along with the following:
1) pencil
2)textbook
3) cell organelle cheat sheet that I have a grade on....this will be the only resource you are allowed to use on the test.....
4) water

Tuesday 1-13-09 HBio Period 6

Journal
Reviewed the glycolysis system
gave you the final exam review
Started your glycolysis project
Gave you the chance to see the ch 6-7 exam

HW: study for the quiz you are having next class
Finish your glycolysis projects
Check FaWeb for any mistakes...if there are mistakes please print out the faweb page and attach the missing assignment that I graded to the printed sheet!

Mon 1-12-08 HBio Period 2+3

Journal
Reviewed glycolysis system
gave you the final exam review
Started your glycolysis project

Gave period 2 the chance to see the ch 6-7 exam

HW:
study for the quiz you are having next class
Finish your glycolysis projects (period 2 will get about 15 min next class to do this) P 3 finish for HW!!!!!
Check FaWeb for any mistakes...if there are mistakes please print out the faweb page and attache the missing assignment that I graded to the printed sheet!

Friday 1-9-08 Hbio

You had a sub today while I was on a field trip

P6:
In class you retook your ch 6-7 exam
HW: NONE

P2:
Took your ch 6-7 exam using notes
HW: NONE

HAVE A GOOD WEEKEND!

Hbio Period 2+3 Jan 8-2009

In class:
turned in flow charts
Journal
Notes on misc. info and glycolysis that I gave you a hand out to follow along with the notes
Started your glycoysis reinforcement activityquestions in class packet 9.5,9.6, Multiple Choice 3,4,5,7

HW: Finish class packet questions listed above

PERIOD TWO:
Be ready with your book and notes on Friday when you will be taking your ch 6-7 exam!!!!!!!

Wed Hbio Period 6 1-7-09

In class:

Journal
Notes on misc. info and glycolysis that I gave you a hand out to follow along with the notes
Started your glycoysis reinforcement activity
questions in class packet 9.5,9.6, Multiple Choice 3,4,5,7

HW: Finish class packet questions listed above

Tuesday 1-6-09 Period 2-3 HBio!!!!!!

GOOD JOB LEARNING AND STAYING ATTENTIVE TODAY!!!!!!!!

In class:
Journal
Misc houskeeping items to talk about
Started Ch 9 notes

Did some practice questions 9.1-9.4 in the class packet

HW:
Finish ws questions 9.1-9.4
Bring your flow charts for the competetion next class

Reminders:

Period 2: You will be taking your open note/book exam on Friday during the rep periods! Come Prepared!

Period 3: You will be taking your open note/book exam on Tuesday 1-13 during the rep periods....come prepared

HBio Period 6 Monay 1-5-09

Journal
Misc houskeeping items to talk about
Started Ch 9 notes
Did some practice questions 9.1-9.4 in the class packet

NO HW!!!!!!!!

Reminder: You will retake your ch 6-7 exam as open note open book on Friday 1-9....come prepared!!!!!!

ALL HONORS BIOLOGY CLASSES

Hey guys:
Long time no see!!!! Hope you all had a great, fun and restful break and are ready to hit the ground running!

The next time I see all of you we will be starting a new chapter. We are going to start Ch 9...cell respiration!

I am going to have all of you take your ch 6-7 exam in class as an open note/open book test because it has been so long since we have talked about this stuff and I want you to do well on this exam and remember the facts to prepare for the CLOSED book final exam that is only TWO WEEKS AWAY!!!!!!

Period 5 you will also get your Scantrons back (I have not graded them yet) and have the opportunity to use your book/notes to fix any questions you would like to fix.

Here are the days each class can expect to redo/take their ch 6-7 open note/book test:

Period 2: I will see you Friday 1-9 during the reps...please plan accordingly
period 3: i will see you Wed 1-13 during the reps......please plan accordingly
period 5: Friday 1-9 during class time

Period 2-3 I am expecting you to all turn in your class flow chart dealing with the cell membrane THURSDAY 1-8!!!!! We will still be using these to count as extra points on the test so there is still a "competition" going on!