Biochem 1 Lecture 7 Hw

A protein has valine as its 25th amino acid. When this amino acid is changed to Alanine, no change to function is noted. Why could this be the case?

Although primary structure is altered, both Alanine and Valine are non-polar amino acids. Thus, it is unlikely other levels of protein structure, and therefore function, would be altered. =>Any change to the amino acid sequence affects the primary structure; however, since the function is identical, we know the change must have not altered the shape of the protein. Often substituting a similar amino acid will have little effect on the protein.

Why should the core of most globular and membrane proteins consist almost entirely of α-helix and β-sheets?

Highly polar N−H and C=O moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein.

An electrostatic interaction might occur within a protein between which of the following amino acid pairs at typical physiological pH? A) Ser/Asn B) Asp/Glu C) Arg/Cys D) Lys/Asp E) Val/Ile

Lys/Asp =>both electrically charged at phys pH (Lys is + / Asp is -)

Globular proteins tend to have what type of functions in the body?

Metabolism and Transport =>Fibrous proteins are typically involved in structure, while globular proteins do the work, such as synthesis, transport, and metabolism.

Would you expect these two tripeptides to have the same function in the body? Why or why not? His-Pro-Val VS Val-Pro-His

No, structure determines function, and their structures are different. =>These two tripeptides have very different structures, thus will not function the same in the body.

_(parallel or anti-parallel)___ β-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and _(parallel or anti-parallel)___ β-sheets are usually arranged with all their hydrophobic residues on one side of the sheet.

Parallel, antiparallel

__(polar &/or nonpolar)__ amino acids are almost never found in the interior of a protein, but the protein surface may consist of __(polar &/or nonpolar)__ amino acids.

Polar, both polar and nonpolar

In sickle cell anemia the 6th amino acid is changed from glutamic acid to valine in the protein hemoglobin. Which level(s) of protein structure could be affected?

Primary, Secondary, and Tertiary =>In sickle cell anemia the shape of the overall protein hemoglobin changes, and as a result has decreased function. The changing of the amino acid changes the primary structure. Additionally, the R group going from a charged group to non-polar group affects the secondary and tertiary structure.

A protein found in the blood (an aqueous environment) has a stretch of its amino acid sequence that is two Valines followed by a Leucine. These amino acids are all found grouped together on the inside of the protein. What level of protein structure does this describe?

Tertiary =>This is describing hydrophobic interactions of the R groups. This is tertiary structure.

Which of the following statements is true about the quaternary structure of a protein? A) based on how subunits interact with one another B) affected by hydrogen bonds C) quaternary structure describes the overall shape of a protein D) driven by a-helices and b-pleated sheets E) found in all proteins

The quaternary structure of a protein is based on how polypeptide subunits interact with one another. =>Only proteins with more than one polypeptide chain have quaternary structure, which refers to the way the polypeptide subunits interact with one another.

The enzyme lactase breaks down lactose into glucose and galactose. The presence of glucose can be qualitatively measured with paper testing strips that turn color to indicate the presence of glucose. The testing strip will change color to purple to indicate glucose is present. If glucose is not present, the testing strip will stay white. In lab, a student heats a sample of the enzyme lactase to 100°C. Next, the lactase is added to a solution of lactose. The student then uses a testing strip to indicate if glucose is present. What should they expect to find and why?

The strip will be white, because no glucose will be produced. The heating will denature lactase, and it will no longer function. =>When proteins are heated to high temperatures they denature, which cause them to unfold. They have lost their structure, and thus their function. Therefore, the strip should show no glucose present, or stay white.

What are the two most common forms of secondary structure in proteins?

alpha-helices and beta-pleated sheets

The outward face of a(n) __(b-sheet or amphiphilic helix)__ consists mainly of polar and charged residues, whereas the inner face contains mostly nonpolar, hydrophobic residues.

amphiphilic helix

All of the following are common denaturing agents except: A) heat B) acidic conditions C) aqueous soln D) basic conditions E) agitation

aqueous solution =>Aqueous solutions alone do interact appreciably with a protein to cause any denaturation of the structure.

What type of interaction would you expect between the R groups, cysteine and cysteine, in tertiary structure?

disulfide bonds =>Cysteines have thiol groups that can interact and form disulfide bonds.

Which of the following is a globular protein? hemoglobin, collagen. amylopectin, keratin, silk

hemoglobin =>Amylopectin is a polysaccharide, and collagen, α-keratin, and silk are fibrous proteins.

What type of interaction holds α-helices and β-pleated sheets together?

hydrogen bonds =>α-Helix and β-pleated sheet structures are stabilized by hydrogen bonds between the amide nitrogen of one peptide bond and the carbonyl oxygen of another peptide bond.

What type of interaction would you expect between the R groups, valine and alanine, in tertiary structure?

hydrophobic =>These both have non-polar R groups and would form hydrophobic interactions.

What type of interaction would you expect between the R groups, lysine and aspartic acid, in tertiary structure?

ion pairing =>Since this is a negatively charged R group paired with a positively charged R group, they will form an ion pair.

Denaturation of a protein by acidic or basic solutions often leads to the breaking of bonds in the protein. Which bond type is most susceptible to denaturation by acids and bases? A) a-carbon to side-chain R group B) a-carbon to amino group C) peptide bond between two amino acids D) a-carbon to carboxyl E) C=O bond in carboxyl group

peptide bond between two amino acids =>Denaturation of a protein by acidic or basic solutions often leads to breaking of bonds in the protein via hydrolysis. The peptide bond between two amino acids forms the primary structure of a protein. This bond is an amide bond which is susceptible to hydrolysis.

What is the name of the a nonprotein group that is bound to a protein and is required for function?

prosthetic group =>The general term for a nonprotein group bound to a protein and required for function is prosthetic group. Substrate and reactant refer to substances acted upon by enzyme proteins, and a cofactor or coenzyme might be a prosthetic group for an enzyme protein, but they are not general terms for any non protein group bound to any type of protein.

Which level of protein structure involves two or more polypeptides interacting through intermolecular interactions?

quaternary =>Quaternary structure occurs when two more polypeptides interact through intermolecular interactions. Only proteins with more than one subunit have this structure.

Electrostatic interactions among amino acid residues on proteins may be damped out by high concentrations of: A) water B) organic solvents C) salts D) heat

salts

Which level of protein structure involves α-helices, β-sheets, and β-turns?

secondary

A major stabilizing factor in the triple helix is a __(linear or staggard)__ structure such that _(gly, lys, or glu)___ residues from the three strands stack along the center of the triple helix.

staggered, gly

Amino acid side chains capable of forming hydrogen bonds are usually located on the protein __(interior or surface)__ and form hydrogen bonds primarily with the __(water solvent or other amino acids)__.

surface, water solvent

Polylysine is a random coil when the pH is less than 11, while it forms an α-helix if the pH is raised to greater than 12. This is because at pH 12:

the lysine residues are neutral which eliminates electrostatic repulsion between the R groups.