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Look at your table of amino acid R-group structures. Which category amino acids are likely to change physical and/or chemical properties if the pH of the surrounding medium changes?

Polar, non charged amino acids.
Basic amino acids.
Non-polar amino acids.

Look at your amino acid structure tables. What category of amino acid is histidine?

basic
non-polar
polar, non-charged

How would Bronsted-Lowry describe histidine?

proton acceptor
proton donor

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Directions: Look at the following amino-acid sequences from two warm-water species and one cold-water species and identify where changes in the sequence occurred.

Line 1: C. punctipinnis: Temperate (cold-adapted)

Line 2: C. caudalis: Tropical (warm-adapted)

Line 3: C. xanthochira: Tropical (warm-adapted)

151

GFERHRVIGS GTNLDSARFR HIMGEKLHLH PSSCHGWIVG EHDGSSVPVW

GFERHRVIGS GTNLDSARFR HIMGEKLHLH PSSCHGWIVG EHDGSSVPVW

GFERHRVIGS GTNLDSARFR HIMGEKLHLH PSSCHGWIIG EHDGSSVPVW

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SGVNVAGVSL QGLNPQMGTD GDSEKWKEVH KLVVDGAYEV IKLKGYTSWA

SGVNVAGVSL QALNPQMGAE GDSENWKAVH KQVVDGAYEV IKLKGYTSWA

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IGMSVADLVE SIMKNLHKVH PVSTLVQGMH GVKDEVFLSV PCVLGNSGLT

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DVIHMTLKPE EEKQLVKSAE TLWGVQKELT

DVIHMTLKPD EEKVLVKSAE TLWGVQKELT

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1. Which amino acids changed between the three species? List four of them below, using the number of the amino acid.

Example: Amino acid 189 changed from valine to isoleucine in a warm adapted species.

1) _______________________________________________________________

2) _______________________________________________________________

3) _______________________________________________________________

4) _______________________________________________________________

2. What were the changes in the chemical properties of the R-groups? Use the amino-acid chart to in the Powerpoint file to answer this question.

Example: Both valine and isoleucine are nonpolar.

1) _______________________________________________________________

2) _______________________________________________________________

3) _______________________________________________________________

4) _______________________________________________________________

3. How might the changes that you identified affect the protein’s structure?

Example: The change would likely have no effect. Neither valine and isoleucine would promote hydrogen bonding with water, because their R groups are nonpolar and thus hydrophobic.

1) _______________________________________________________________

2) _______________________________________________________________

3) _______________________________________________________________

4) _______________________________________________________________

4. Assuming that the mutations are adaptive, how should the changes that you identified affect the stability of the protein at low and high temperatures?

2. Let’s consider transport of iodine (I- ) into your thyroid cells. You need iodine in your diet for normal thyroid activity, but dietary iodine concentrations are very low (usually in America we get enough just from what is added to iodized salt). People have been interested for some time in trying to figure out how we can transport iodine so efficiently. One way we can study the transporter is to look for mutations that alter its function, and therefore lead to thyroid problems.

A. The transporter is a rocker-switch type Na+ / Isymport. The pivot of the rocker mechanism is a glycine amino acid, #93 in the primary structure of the transporter. Some people with thyroid problems have a mutation that changes this glycine to an arginine. Define what is meant by “the primary structure” of the transporter. Explain how that change would alter the function of the transporter. (You may consult the structure of arginine on slide 7 of Lecture 3.)

B. There is normally an Arginine at position #124 in the primary structure of the transporter. This Arginine participates in hydrogen bonding with an Asparagine, positioned at #441 in the primary structure. There is evidence that these H-bonds are present in the outward-facing transporter conformation, but are broken when the transporter switches to the inward-facing conformation. People with mutations that replace Arginine 124 with Histidine have difficulty transporting Iodine into their thyroid cells. Copy the structures of Arginine and Asparagine. Label relevant H-bond donor and acceptor atoms between these two amino acids. Explain how replacing Arginine 124 with Histidine could affect the operation of the transporter. (Make a sketch of the transporter in the inward-facing and outward-facing conformations to help you to visualize this.)

C. Recent investigation demonstrated that there are actually TWO Na+ ions symported with the Iion. When a colleague of mine saw this report, he said “Ah ha! So that’s why iodine transport is so efficient!” Explain why it would make a difference whether one or two sodium ions were involved? Why would involving two sodium ions make the transporter more efficient?

I JUST NEED SIMPLE/BASIC ANSWERS NOT LONG ANSWERS

1. Explain how life can be viewed at different levels of biological complexity.

2. Explain how researchers study biology at different levels, ranging from molecules to ecosystems.

3. Distinguish between discovery-based science and hypothesis testing, and describe the steps of the scientific method.

4. Tell whether a given topic or research study is about biology. Tell whether that study is discovery-based or hypothesis testing, or both.

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Relate atomic structure to the periodic table of the elements. List the elements that make up most of the mass of all living organisms.

Explain how a single element may exist in more than one form, called isotopes, and how certain isotopes have importance in human medicine.

Compare and contrast the types of atomic interactions (bonds) that lead to the formation of molecules.

Tell which atoms and how many of each make up a given molecule (formula or diagram).

For a bond in a given molecule, tell whether the bond is covalent, and if it is, tell whether it is polar or nonpolar and why you think so.

Explain the concept of electronegativity and how it contributes to the formation of polar and nonpolar covalent bonds. Tell whether a given atom is electronegative or not, and why you think so. Label partial charges in a polar bond.

Draw five water molecules and label the atoms and bonds within and between the 5 molecules.

Describe how hydrogen bonding determines many properties of water.

List the properties of water that make it a valuable solvent, and distinguish between hydrophilic and hydrophobic substances.

Explain how water has the ability to ionize into hydroxide ions (OH–) and into hydrogen ions (H+), and how the H+ concentration is expressed as a solution's pH.

Explain the properties of carbon that make it the chemical basis of all life.

Describe the variety and chemical characteristics of common functional groups of organic compounds.

Diagram how small molecules may be assembled into larger ones by dehydration reactions and how hydrolysis reactions can reverse this process.

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If shown an organic molecule, tell whether it is an amino acid, nucleotide, fatty acid, steroid, monosaccharide or disaccharide and how you know.

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List the several different classes of lipid molecules important in living organisms.

Diagram the structure of a triglyceride and explain how it is affected by the presence of saturated and unsaturated fatty acids. Explain why some fats are solid at room temperature, and others are liquid.

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Tell how certain bases pair with others in DNA and RNA.

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Outline the differences in complexity among bacteria, animal, and plant cells.

Describe how a eukaryotic cell can be viewed as four interacting systems: the nucleus, cytosol, endomembrane system, and semiautonomous organelles.

Explain how the proteome underlies the structure and function of cells.

Analyze how cell size and shape affect the surface area/volume ratio.

Identify the location of the cytosol in a eukaryotic cell and list its general functions.

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