Biology 1115 Ch 3 + 4 Learning Outcomes

Explain how a huge diversity of polymers can arise from a small number of monomers.

Monomers can take on different forms of themselves and thus have the potential to create many combinations of monomers.

Describe the structure of an amino acid.

An amino group (NH2, basic) and a carboxyl group (COOH, acidic) separated by a carbon attached to a hydrogen and a specific side chain or R group.

Recognize whether an R group is charged, polar, or nonpolar, and describe how this impacts the role of that R group in protein folding.

Charged R groups contain carboxyl groups or amino groups (when ionized, show a charge).

Polar R groups contain oxygen or nitrogen atoms with partial charges.

Charged and polar R groups interact positively with the surrounding water. The entire chain twists until the maximum number of these groups are in full contact with the surrounding water. This supports the huge protein molecule and helps keep it in solution.

Nonpolar R groups have no charge and little to no amount of oxygen or nitrogen.

Nonpolar R groups are hydrophobic so these R groups become buried deep within the folded protein because they want to stay as far away from the water as possible. These forces help hold the 3D structure of the protein.

Explain how amino acids are linked together to form polypeptides.

They polymerize through dehydration synthesis. The amino group of one amino acid loses a hydrogen and the carboxyl group of another amino acid loses an oxygen and a hydrogen to form water and thus create a peptide bond between the nitrogen on the amino group and the carbon on the carboxyl group.

Describe the 4 levels of protein structure, including the interactions involved in each.

Primary: unique sequence of amino acids

Secondary: Hydrogen bonds form between the backbone and take the form of a helix or pleated sheet

Tertiary: Interactions between R groups, or between R groups and the backbone cause the backbone to bend and fold which contributes to the final 3D shape of the protein

Quaternary: When 2 or more folded polypeptide chains form one functional macromolecule.

Explain how proteins can become denatured.

Proteins can become denatured by changes to their environment such as pH, temperature, or salt concentration. These environmental changes disrupt the interactions that determine secondary and tertiary structure and cause the protein to unfold.

Describe the structure of a nucleotide.

A nucleotide consists of 3 components. A phosphate group, a pentose (5-carbon) deoxyribose sugar, and a nitrogenous base.

Distinguish between pyrimidines and purines, and list the nitrogenous bases that fall into each category.

Pyrimidines: Cytosine, thymine, and uracil. A single 6-membered ring.

Purines: Adenine and guanine, A 6-membered ring fused to a 5-membered ring.

Distinguish between ribose and deoxyribose.

Ribose: found in RNA

Deoxyribose: found in DNA, lacks an oxygen atom

Distinguish between the 5' end and the 3' end of a nucleotide/polynucleotide.

The pentose or deoxyribose sugar has 5 carbons. The number corresponds to the location of the carbon on the 5-carbon ring. Both the 3' end and 5' end connect to the neighbouring nucleotide via phosphodiester bonds.

Explain how nucleotides are linked together to form polynucleotides.

Through phosphodiester bonds between a phosphate group of one nucleotide and the 3' end and 5' end of a pentose sugar on other nucleotides.

Describe complementary base pairing, and explain only certain bases pair with one another.

Complementary base pairing is the pairs of nitrogenous bases that can only bond with each other. The 2 factors that determine this are space and atomic structure. 2 bases of the same family (pyrimidines/purines) cannot bond with each other as they would either take up too much space or have too much space between them. Each base also have certain atoms at the ends that bond with other bases. When cytosine pairs with guanine, 3 hydrogen bonds are formed. When adenine pairs with thymine or uracil, only 2 hydrogen bonds are formed.

Differentiate between DNA and RNA with respect to general function, structure of nucleotide, secondary structure, and tertiary structure.

General Function: DNA = store and transmit biological information, RNA = protein synthesis/DNA replication

Secondary Structure: DNA = 2 polynucleotide chains running antiparallel to one another in the form of a double helix, RNA = a single polynucleotide chain that runs antiparallel to itself by shaping itself into a "hairpin"

Tertiary Structure: DNA = double helixes wrap around proteins to take on a more compact form, RNA = fold up further into a huge diversity of 3D tertiary structures, allowing for RNA to take on a diverse array of shapes and functions (e.g. mRNA, tRNA, rRNA)