Question 1.

A strain of E. coli carries a substitution mutation causing the terminator codon 5’-UAG-3’ to occur at an interior position in a particular type of mRNA. This strain also carries a suppressor mutation that alters the anti-codon of a type of tRNA molecule so that it reads 3’-AUC-5’. This type of tRNA reads this terminator codon and inserts the amino acid tyrosine.

a.What effect would the presence of both of these mutations together have on the polypeptide translated from the mRNA carrying the mutant terminator codon?

b.Do you expect that there might be other genes whose translation would be altered by the presence of the tRNA produced by this suppressor gene? If so, describe the circumstances under which translation would be altered and explain how it would be altered.

Question 9

Analysis of the cellular structure of Chewbacca (a Wookie) showed that most of the basic cellular and molecular processes are the same between Wookies and humans, much as they are the same between humans and other closely related organisms. Many proteins are highly conserved and basic cellular metabolism is maintained. Interestingly, one new organelle is present, which researchers named the Wookiesome. Many of the proteins found within the Wookiesome have the eight amino acid sequence “HARRIEST”. You make a hypothesis that this region is important for organelle import.

(A) Design an experiment to indicate if “HARRIEST” is necessary for organelle import.

(B) Design an experiment to indicate if “HARRIEST” is sufficient for organelle import.

(C) Explain how it is possible that the sequence could be necessary but not sufficient.

4. Explain how it is possible that the sequence could be sufficient but not necessary

1) a mutation occurs in which an AAA codon, which signifies lysine, into AGA which signifies a chemically similar amino acid arginine. This is an example of a ____ mutation?

a) conservative nonsynomous b) frameshift   c) nonsense   d) conditional   e) silent

It has to be neutral mutation, but the option for neutral is not given... would it be conditional?

2) Which of the following types of inheritance could account for an affected male having all affected daugters but no affected sons?

a) autosomal recessive   b) autosomal dominant   c) Y-linked   d) X-linked recessive   e) X-linked dominant

it has to be dominant... so its either b or e?  

3) The site where RNA polymerase binds to the DNA template is called the ____ sequence.

1)         Predict (write the sequences of) the fragments that would be generated from the treatment of

            the following peptide

Gly-Ala-Trp-Asp-Arg-Lys-Ala-Glu- Gly-Phe-Gln

            with:

            a) trypsin (4 pnts)

            b) chymotrypsin

            c) pepsin

2)         A certain protein has an α-helix which is 18 residues long with the sequence shown below.

            It is known that hydrogen bonding through the backbone H-bond donor/acceptor groups

            stabilizes most of the structure. Show what other interactions would help stabilize the helix

            by drawing lines (or brackets) between the interacting amino acid residues and naming the

            type of interaction involved.

Q         L          A         N         R         Y         R         T         D         L          E          Q         K         W        Q         N         E          P

You are trying to determine the structure of a protein that you know is pure. You carry out a series of experiments on this protein. The results are listed below.

Describe what you can determine about the protein’s structure. (For example, what can you determine about the protein’s molecular weight, primary, secondary, tertiary, quaternary structure?)

· Size exclusion chromatography of the native protein indicates an apparent molecular weight of 160,000.

· SDS polyacrylamide gel electrophoresis of the protein carried out WITHOUT the addition of a disulfide-bond reducing agent shows the protein as having an apparent molecular weight of 80,000. After treatment with performic acid, the same technique reveals two bands of molecular weights 35,000 and 45,000.

·The Sanger reagent (fluorodinitrobenzene) identifies Ala and Leu as amino terminal residues, in roughly equal amounts.

1.- Why can ruminant herbivores use ammonia or urea (non-protein nitrogen) as a valuable nutrient? What happens to post-gastric fermenting herbivores, such as horses, when they eat a diet containing high levels ammonia? Why?

2.- Hummingbirds are very small birds (about 10 grams) that are extremely active in the wild and often spend winters in relatively cool places like Davis. Humans like you stay in Davis during the winter too.

A) The maintenance energy requirements of adult hummingbirds (kcal per gram body weight per day) are very high compared to humans. Why is this?

B) Why can hummingbirds that live in Davis meet their amino acid requirements eating foods that have very low levels (5) of protein?

1. Antibody is prepared to the thr repressor protein isolated from a wild-type strain.  Competetive antibody binding assays show that several times more repressor is present in an extract prepared from the derepressed mutant described above than in an extract prepared from the wild-type strain.  What is your interpretation of these data?
2. The repressor protein requires a pH of 6.1 for optimal binding to its operator in vitro.  If the pH goes above pH 8.0, the repressor is unable to bind.  What amino acid side chains are implicated?  Why is binding reduced in alkaline media?
3. What effect would an increase in pH have on cell transcription of the thr operon? Why?
4. What percentage of the repressor will bind at pH 6.3?  More than 50% or less?  Now calculate.

How can it be determined if an apparently normal dog is carrying a gene for deafness?

Phenylketonuria (PKU) is a defect of amino acid metabolism inherited as an autosomal recessive trait. Untreated children are usually severely mentally retarded. If two phenotypically normal parents have a PKU child, what are the genotypes and phenotypes of their children and in what portions?

Cystic fibrosis, inherited as an autosomal recessive trait, involves a defect of glycoprotein metabolism. Phenotypically normal parents had two children, one normal, one with cystic fibrosis. Write the probable genotypes for the parents

In man, hemophilia (failure of the blood to clot normally) is inherited as an X-Linked recessive trait. A woman has one hemophiliac son. Write the genotypes for the women, her son, her normal husband, and other children the women might have.

Treatment of a polypeptide with Tris-(2-carboxyethyl)-phosphine hydrochloride (TCEP) yields two peptides:

1. I-Q-K-H-C-R-C-A-K-M-V-S

2. F-C-R-L-K-D-C-K-N-D

Treatment of the intact polypeptide with Trypsin yields fragments with the following amino acid composition:
(Ser, Met, Val) (Lys, Gln, Ile) (Phe, Ala, Cys2, Arg, Lys) (Asp, Asn) (Leu, Lys)
(Lys, His, Asp, Cys2, Arg)

a) The intact (untouched) polypeptide is labeled with 1-Fluoro-2,4-dinitrobenzene (FDNB) labeling, followed by acid hydrolysis. What will be observed?

b) Name and briefly describe a method which may determine if the intact polypeptide was a monomer or a dimer

Disc 1

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The following Critical Thinking questions are meant to provide deeper understanding of biology topics after students have watched this week's Panopto lectures. Attempting to answers these before lectures have been watched, may compromise your understanding and participation in this course.

In the future, I will be subdividing the class into smaller online groups to answer these questions so it may be less intimidating for the "shy" person, but for this first one I wanted to do it as a class.

How do your get graded? Well, you are NOT graded on whether you answer the questions correctly! You are graded on how well you use critical thought from our lecture and chapter readings to synthesize answers. Your posts should NOT be long, multi-paragraph essays but rather concise statements that are well thought out. They can even be in the form of a question or inquiry such as "...I know that only proteins have disulfide bridges so if a stain binds to these groups then it should change color, however I'm not sure how that relates to the question...". Help each other out if some people are struggling to understand the question or are having difficulty seeing a point of view. Some questions may not have a correct answer! I will reveal the answers or possible answers after the due date.

For each question below post one critical thinking post and one critical thinking reply to another student before the due date (that's a total of 8 posts all together). Note that your posts doesn't have to answer the question completely...partial answers to a question are fine!

Macromolecules

1. Trans-fatty acids are a type of unsaturated fat. Most trans-fats consumed today are industrially created as a side effect of partial hydrogenation of plant oils (Crisco). In trans-fat molecules, the hydrogens on the doubly bonded carbon atoms (characteristic of all unsaturated fats) are straighter, rather than kinked, in shape. Why do you think trans-fats are considered unhealthy as compared to other unsaturated fats? Can you explain your answer chemically?
2. Why might an evolutionary biologist be interested in comparing the amino acid sequence of proteins between two different species? What differences might she find when comparing species that are distantly related or closely related? Explain.
3. Some viruses carry their genetic material as DNA while others, known as retroviruses, carry their genes as RNA. Virologists studying emerging viruses that might infect humans are interested in discovering which types would be the most difficult for our immune system to fight. Viruses that mutate quickly and thus, are able to thwart our immune defenses are the most concerning. Which of these two viruses, DNA or RNA, do you think mutate faster? Explain.