Biology Exam Paper

Length:  By the time you answer each question, you should have 5 solid paragraphs, or about 2 and 2 ½ -3 pages double spaced.  If you are looking for a word count, I would like 600+ words.

Directions: Answer the following questions (2 – 5 sentences) in your own words. Type your answers beneath each question and upload your document through Blackboard before the due date/time.

Proteins are biological macromolecules made from smaller building units called amino acids. There are 20 natural occurring amino acids which can combine in various ways to form a polypeptide. There are four distinctive levels of protein structure: primary, secondary, tertiary and quaternary. The primary structure of a protein is important in determining the final three dimensional structure and hence the role and function of a particular protein, both in the human body and in life around us. The secondary structure of a protein can fall into two major categories; α-helices or β-sheets, other variants also exist such as β-turns {{20 Brändén, Carl-Ivar, 1934- 1991}}. The precise folding or these secondary structures into a three dimensional shape is known as the tertiary structure of a protein and multiple polypeptides bound together via covalent and non-covalent bonds forms the complex quaternary structure of a protein.

DNA replication is an intricate process that requires many different proteins. Each protein preforms a very specific function in the creation of a new DNA strand. First helicase works by unwinding or dividing the original double helix into single stands. The point where the DNA is separated by the helicase is known as the replication fork. Single strand binding proteins attach to the newly made single strand of DNA to prevent re-annealing. Next is the addition of an RNA

. The 3-D tertiary structure of polypeptide proteins globular and is the result of interactions that occur between R groups. Tertiary structure is a result of the bonds between sidechains of amino acids, the R groups. The structure and bonds involve alpha helices, beta pleated sheets, and also regions unique to each protein. Tertiary proteins are held together by four different types of forces; hydrogen bonds, hydrophobic interactions (including Van der Waals interactions), ionic bonding (electrostatic interactions), and disulfide bridges (strong covalent bonds). Hydrogen bonds occur within and between polypeptide chains and the aqueous environment. Hydrogen bonding forms between a highly electronegative oxygen atom or a nitrogen atom and a hydrogen atom attached to another oxygen atom or a nitrogen atom. This links the amino acid

Read each question carefully and answer only the question that is asked. Answers for each question should be 2 pages, typed, Times New Roman, 12 point font, double spaced, with one inch margins. This document is already formatted correctly.

Select the one BEST answer to each question below. This is an open-book quiz. Students may consult their textbooks and their own class notes while taking this quiz. Students may not consult any other resources, including other students, either in person or by electronic means.

(a) Describe THREE types of chemical bonds/interactions found in proteins. For each type, describe its role in determining protein structure.

Proteins are polymeric chains that are built from monomers called amino acids. All structural and functional properties of proteins derive from the chemical properties of the polypeptide chain. There are four levels of protein structural organization: primary, secondary, tertiary, and quaternary. Primary structure is defined as the linear sequence of amino acids in a polypeptide chain. The secondary structure refers to certain regular geometric figures of the chain. Tertiary structure results from long-range contacts within the chain. The quaternary structure is the organization of protein subunits, or two or more independent polypeptide chains.

addition, there seem to be several hydrogen bonds between the protein and the phosphate backbone of the DNA such as the oxygen in the phosphate group at position 33.

Chromosome (A75): DNA is wrapped around proteins like thread around a spool and compacted into structures called chromosomes.

These proteins differ depending on their function in the cell, but often prevent misfolding of nascent protein, and assist in refolding of the misfolded proteins. Protein folding is dependent on the amino acid sequence within the polypeptide chain that is synthesized from the DNA strand in the ribosome.2 Upon release from the ribosome, the polypeptide chain undergoes a series of conformational changes based on the amino acid sequence to produce a functional protein structure. The assembled native protein is directed to the ER via vesicle

Crick, F. H., et al. General Nature of the Genetic Code for Proteins. Nature 192, 1227–1232 (1961). doi:10.1038/1921227a0.

The structure of an enzyme as protein has a primary, secondary, tertiary, and sometimes quaternary structure. The primary structure of an enzyme, like any protein, is the order of its amino acids. The secondary structure involves alpha helices and beta pleated sheets. Alpha helices are a coil that is formed by hydrogen bonding between every fourth amino acid. Beta pleated sheets are formed by hydrogen bonding between two or more parts of the polypeptide chain that are side by side. The tertiary structure contains disulfide bridges, ionic bonds, hydrophobic interactions, and hydrogen bonds. Disulfide bridges are the result of two sulfhydryl groups interacting because the the folding of the protein. Ionic bonds can form between polar groups on amino acids. Hydrophobic interactions are the cluster of amino acids with nonpolar side chains that is commonly seen in proteins. Hydrogen bonds can also form. The quaternary structure of an enzyme is when multiple proteins are bonded together in one complex made of proteins subunits.

In most instances, protein molecules are usually embedded from hundreds to thousands of amino acids. A repertoire of twenty different amino acids, joined in any possible sequence allows the existence of an inconceivably large number of proteins that is infinite in nature.