BIOCH 200 Unit 1 - Biomolecules (Questions)

Are lipids monomers? Do they form polymers?

No, there are lipid building blocks (fatty acid etc.) that build larger molecules (ex. cholesterol), but they are not classified as polymers or monomers

Describe how biomolecules are classified, with distinguishing characteristics of each class.

Four major classes:

1. Amino acids (must contain nitrogen from amino group)

2. Carbohydrates (contain only carbon, hydrogen, oxygen)

3. Nucleotides (must contain nitrogen and phosphorus from nitrogenous base and phosphate backbone)

4. Lipids (hydrophobic/contain only carbon and hydrogen)

Describe the general structure of a carbohydrate, including functional groups, amounts, and structure. What is its general formula?

(C x H₂O)n, where n is a number from 3-9. Unbranched carbon chain typically found as a ring structure in solution. (n-1) hydroxyl groups and contains a carbonyl: will be an aldehyde if terminal, will be ketone on any other

In structural diagrams, which colours correspond to: O, C, H, N, S, P?

O: red

C: black

H: white

N: blue

S: yellow

P: orange

Under most biological conditions, what form will carboxyl groups appear in? Which form will amino groups appear in?

Charged/basic form for both (COO^-/NH₃⁺)

Describe how an ester linkage is formed, including reactions and groups.

A hydroxyl group is removed from a carboxylic acid group and a hydrogen is removed from a hydroxyl group in a dehydration reaction, precipitating a water molecule. The acyl group formed from the carboxylic acid attaches to the oxygen from the hydroxyl group, forming an ester linkage (C-O) to create an ester functional group

Describe how an amine linkage is formed, including reactions and groups.

A hydroxyl group is removed from a carboxylic acid group and a proton is removed from an amino group in a dehydration reaction, precipitating a water molecule. The acyl group formed from the carboxylic acid attaches to the central nitrogen from the amino group, forming an amide linkage (N-O) to create an amide functional group

How does a monomer differ from a residue?

Residue: monomer inside chain. Monomer on its own will behave differently as it does not have covalent bonds/linkages found on residues

What is the directionality of polymers? Why is this important? Why does it happen?

All covalent bonds are formed in the same orientation. Explains directionally orientated formation of molecules such as 5’ to 3’ DNA, C to N protein formation. Ends are geometrically distinct

How can an uncharged molecule have a permanent dipole?

Atom with high electronegativity covalently bonded to an atom with low electronegativity, causing electron density to be permanently pulled to one atom stronger than the other (partial -, partial +)

Which atoms accept hydrogen bonds? Which atoms donate/form them?

An electronegative atom (O, S, N) with a lone pair of electrons is able to accept hydrogen to form hydrogen bonds. An electronegative atom covalently bonded to a hydrogen is able to donate the hydrogen to form hydrogen bonds

Describe the relative lengths of hydrogen and covalent bonds. Why?

Hydrogen bonds are shorter than covalent bonds, as they are weaker (intermolecular) while covalent bonds are strong (intramolecular)

Compare the strength/amount of hydrogen bonds formed in ice vs in free-flowing water. Why, using structure?

In ice, each water molecule forms 4 H-bonds as the electrostatic interaction is strong and stable. In water, each molecule forms ~3 H-bonds as the electrostatic interaction is weaker and less stable.

In ice, there is a regular lattice of H-bonds as the ice forms water crystals, thus the hydrogen bonds are more energetically stable. In water, there is a constantly changing fluctuating H-bond structure with more energy (heat), and thus the H-bonds are less energetically stable

In hydrogen bond formation, do acceptors/donors act as strong or weak acids/bases? Explain.

Weak: tries to fully donate/accept hydrogen but is unable to and thus shares the hydrogen between, forming an electrostatic interaction

Rank the types of non-covalent interactions in terms of strength. Are they bonds? How numerous is each compared to covalent bonds, and why is this important?

Strongest: ionic interactions, hydrogen bonds, dipole-dipole, london dispersion. No, they are interactions and are much weaker than covalent bonds

Van der waals and H-bonds are most numerous, followed by ionic interactions still being more numerous than covalent bonds. Non-covalent interactions are important due to how numerous they are, which arises from their weakness causing them to be easily formed and broken

A molecule’s solubility in water depends on ___.

Polarity: Its ability to bond with water (H-bonds, dipole)

Explain the reasoning behind the hydrophobic effect. How do nonpolar molecules affect the entropy of water?

Water forms a shell around nonpolar molecules, and the water molecules in this shell are constrained (difficult to create and break H-bonds with them). When nonpolar molecules are all separately placed in water, lots of shells are created and thus there is lots of constrained water molecules which is unfavourable for water. Pushing the hydrophobic molecules together allows less constrained molecules.

Nonpolar molecules increase entropy of water via the hydrophobic effect pushing them to a more favourable conformation → more energetically favourable. (Hydrophobic effect more entropically favourable)

Amphiphathic/amphiphillic molecules aggregate in water to position ___ parts close to water and ___ parts away from water.

Polar, nonpolar

Fatty acids form ___ in water while membrane lipids form ___ in water. Why does each form each respective shape?

Micelles, bilayers. Fatty acids have a narrower nonpolar tail and a wider polar head, which allows the tails to be sandwiched inside a fully rounded micelle ball shape. Membrane lipids have heads and tails of relatively equal width, meaning the heads will line up with the tails to create a bilayer instead of rounding in to form a micelle