Give the hexapeptide sequence that gives the following fragments on limited acid hydrolysis:

Use the single letter abbreviations for amino acids.

Fragment 1: Pro-Leu-Gly
Fragment 2: Arg-Pro
Fragment 3: Gly-Ile-Val

Hexapeptide:

13. Describe the sodium-potassium pump, including all players involved, and what the function is 16. Name 3 components that contribute to the structure of the plasma membrane 17. Draw and label the reaction of the formation of a peptide bond with two generic amino acids

Leigh syndrome is a progressive brain disease that first manifests in individuals between the ages of 6-36 months. Most patients with Leigh syndrome die at a young age. Individuals with Leigh syndrome have a defect in their mitochondrial function.

About 15% of individuals with Leigh syndrome carry mutations in their SURF1 genes.  The SURF1 gene is located on the long arm of chromosome 9 and encodes a protein that is essential for assembling one of the respiratory chain complexes, complex IV, located in the inner mitochondrial membrane.

a. Consider the following processes. Would each occur at a higher rate, lower rate or normal ratein a person with Leigh syndrome compared to a person without the syndrome? Explain briefly (4 pts)

Glycolysis

Pyruvate oxidation

Citric Acid cycle

ATP production by ATP synthase

b. Patients with Leigh syndrome may also suffer effects from acidosis, characterized by low pH in body tissues and blood. Why would patients with Leigh syndrome have acidosis? Explain briefly (2 pts)

c. Some metabolic disorders can be alleviated by giving the patient a specialized diet. Fats are broken down to fatty acids & glycerol in the liver, and through a process, beta-oxidation into acetyl CoA. If glucose and fat sources are depleted, amino acids can also be converted into molecules that can enter the TCA cycle. Would a low-carbohydrate, high-protein and high-fat diet help individuals with Leigh syndrome? Explain briefly. (2 pts)

Data Tables and Post-Lab Assessment

Lab Questions

1.     Transcribe the following DNA sequence:

Hb A:

5’ AGT AAC GGC AGA CTT CTC CTC AGG AGT CAG GTG CAC CAT 3’

3'UCA UUG CCG UCU GAA GAG GAG UCC UCA GUC CAC GUG GUA 5'

2.     Translate your new RNA sequence using the genetic code. Remember that when determining your amino acid sequence, the RNA sequence is read from 5’ to 3’.

val- val -his- val- ser -ser- glu- glu- ser-ser- pro- leu -ser

Note: the first amino acid will be Met.

3.     Transcribe the following DNA sequence.

Hb S:

5’ AGT AAC GGC AGA CTT CTC CAC AGG AGT CAG GTG CAC CAT 3’

3`UCA UUG CCG UCU GCC GAG GUG UCC UCA GUC CAC GUG GUA 5`

4.     Translate your Hb S transcript.

val- val- his- val- ser-ser-val-glu- ser- ser- pro- leu - ser

Note: the first amino acid will be Met.

Post-Lab Questions

1.     How long are each of your peptide chains (how many amino acids are present)?

The proteins are made up of multiple units of amino acid. When we talk about peptide

chains they are combination of multiple amino acids. Each of the peptide chain consists

of many amino acids and the number varies.

2.     What differences exist between your two transcripts? What about your translated product?

3.     Hb A represents a section of the 626 base normal hemoglobin beta mRNA sequence. Hb S is from the sickle cell hemoglobin. Is the mutation found in sickle cell hemoglobin a point mutation or a frameshift mutation?

4.     Does the sickle cell mutation result in a missense mutation, silent mutation or nonsense mutation? Why?

A missense mutation is the cause of the disease, sickle cell anemia In a missense mutation, a change in one base pair causes a single amino acid to be changed in the resulting protein. In sicle cell anaemia there is missence mutation in ?-globin gene where glutamic acid (E/Glu) being substituted by valine (V/Val) at position 6.

1. What are some of the functions of lipids in the body?

2. Draw an example of each type of the following lipids: a. Fatty acid (saturated and unsaturated) b. Prostaglandin c. Wax d. Triacylglycerol (Fat and oil) e. Glycerophospholipid f. Sphingolipid g. Steroid

3. How do saturated and unsaturated fatty acids differ? What factor(s) affect the difference(s) in melting points of saturated and unsaturated fatty acids of the same carbon chain?

4. Draw the condensed structural formula for the ester formed from 3 moles of stearic acid and glycerol.

5. Draw the structural formula for the product of the hydrogenation of the following triacylglycerol:

6. Identify the following features of the phospholipid below: a. Is the phospholipid formed form glycerol or sphingosine? b. What are the fatty acids? c. What type of bond connects the fatty acid? d. What is the amino alcohol? e. What type of bond connects the amino alcohol?

7. What is the major function of cholesterol in the body?

8. What is the function of bile salts in digestion?

9. What is the function of the lipid bilayer?

10.Identify the type of transport described by each of the following: a. an ion moves from low to high concentration in the cell. b. carbon dioxide moves through a cell membrane. Amino Acids and Proteins 1. What functional groups are found in all amino acids? 2. Draw the structure of each amino acid below at low pH (pH = 1), pH = 7.4 and high pH (pH = 14) and classify it as polar or nonpolar. If polar, indicate if the R group is neutral, acidic or basic. Indicate if each is hydrophobic or hydrophilic. a. lysine b. proline c. valine d. tyrosine 3. Define the following: a. Zwitterion b. Isoelectric point 4. Draw the condensed structural formulas for each of the following peptides and give the three-letter and/or one-letter abbreviations: a. prolylaspartate b. threonylleucine c. methionylglutaminyllysine d. histidylglycylglutamylisoleucine 5. What is the difference in hydrogen bonding between and alpha-helix and a beta-sheet? 6. Indicate whether each of the following statements describes primary, secondary, tertiary or quaternary protein structure: a. Hydrophobic R groups seeking a nonpolar environment move toward the inside of the folded protein. b. An active protein contains four tertiary subunits c. Valine replaces glutamate in the beta-chain. d. Protein chains of collagen form a triple helix. 7. What structural level of protein is affected by hydrolysis? (primary, secondary, tertiary and/or quaternary) 8. Note the 5 types of denaturation and an example of each. 9. How does denaturation of a protein differ from its hydrolysis?

If the DNA sequence in the question above is at the BEGINNING of a gene, what are the first 2 amino acids that will be joined at the ribosome? Remember there is a START codon. Use the information on this chart to answer the question.

asparagine, alanine

methionine, glutamine

leucine, alanine

alanine, lysine

methionine, asparagine

Protein-Energy malnutrition (PEM) is a common manifestation in cirrhotic patients with a reported incidence of 65 – 90%. One treatment technique is to add branched chain amino acids and/or their keto analogs to the diet. Why do you think clinicians use this as a potential treatment?

1. Monosaccharides can be joined together by a process called

2. When two monosaccharides are joined together, the resulting molecule is called a(n)

3. What is the name of the covalent bond that joins two monosaccarides?

4. Select all the disaccharides:

5. The covalent bond that joins glycerol and a fatty acid together (once dehydration synthesis has occurred) is called

6. What two functional groups are present in all amino acids?

7. The covalent bond that joins amino acids together (once dehydration synthesis has occurred) is called

8. DNA contains the sugar ___ whereas RNA contains____.