MOL100 Chemical Foundations of Molecular Biology - Lecture 2

Flashcards covering key concepts from MOL100 Lecture 2 on Chemical Foundations of Molecular Biology and Chemical Building Blocks of Cells.

What are the two fundamental types of cells discussed?

Prokaryotic cells and Eukaryotic cells.

Name some key organelles found in eukaryotic cells.

Nucleus, ER, Golgi, Lysosomes, cytoskeleton, and cell junctions.

What are the four main macromolecules of life?

Proteins, Nucleic acids (DNA + RNA), Phospholipids, and Saccharides (sugars).

What three fundamental particles make up an atom?

Protons, neutrons, and electrons.

Where are protons and neutrons located within an atom?

They form the nucleus.

What is the maximum number of electrons that one orbital can contain?

Two electrons (forming an electron pair).

How do electron pairs form covalent bonds?

An electron from one atom forms a pair with an electron from a second atom, and this shared pair constitutes a covalent bond.

What element is a key atom in organic biomolecules, and how many covalent bonds can it typically form?

Carbon, which forms four covalent bonds.

What is a characteristic of double bonds in molecules?

Double bonds cannot rotate.

What is an asymmetrical carbon atom?

A carbon atom that is bound to four different atoms or groups of atoms.

What is chirality?

The property of a molecule with an asymmetric carbon atom to exist as two different mirror-image forms (stereoisomers).

How can stereoisomers differ dramatically in their biological activity?

As shown with thalidomide, where S-thalidomide caused limb malformations, while R-thalidomide did not.

What determines if a covalent bond is polar or nonpolar?

The similarity in electronegativity between the two atoms forming the bond. If similar, the bond is nonpolar; if dissimilar, it's polar.

What is an electric dipole in the context of a polar bond?

A molecule with separated partial positive and negative charges due to differences in electronegativity, such as H2O.

What is a key difference between covalent and non-covalent interactions regarding electron involvement?

Covalent bonds involve shared electrons, while non-covalent interactions do not involve shared electrons.

Why are non-covalent interactions important in macromolecules, despite being individually less stable?

Many non-covalent interactions acting together stabilize the 3D structure of macromolecules and facilitate interactions between them.

How do electrostatic (ionic) interactions form?

They form between oppositely charged ions (cations and anions) resulting from the transfer of electrons between atoms.

How do hydrogen bonds form?

They form when a partially positively charged hydrogen atom (bonded to a highly electronegative atom) interacts with electrons from another atom.

What causes van der Waals interactions?

The constant movement of electrons creating transient differences in charge (transient dipoles), which then interact.

Describe characteristics of van der Waals interactions.

They are very weak, act only at very short distances, and occur in both polar and non-polar molecules.

What happens when nonpolar molecules like fatty acids are in water?

H2O molecules form 'cages' around them, and this aggregation of nonpolar molecules (hydrophobic effect) reduces the number of H2O molecules required to form these cages, making it energetically favorable.

What is molecular complementarity?

The fit between molecules determined by numerous non-covalent interactions, which dictates the 3D structure of macromolecules and their binding affinity.

What are polymers, and how are they formed from monomers?

Polymers are large molecules consisting of many small subunits called monomers, which are connected by covalent bonds.

What are the monomeric subunits of proteins?

Amino acids (aa).

What four chemical groups are bonded to the central alpha carbon (Cα) of an amino acid?

One amino group (-NH2), one carboxyl group (-COOH), a hydrogen atom (-H), and one variable group (-R) called the side chain.

How do amino acids bond to each other to form proteins?

Via peptide bonds.

How are amino acids generally classified based on their side chains?

Into four broad groups: acidic, basic, polar, and nonpolar.

Which types of amino acids are hydrophilic?

Amino acids with basic (positively charged), acidic (negatively charged), or polar (but not charged) side chains.

Which unique property does Cysteine possess?

It can form covalent disulfide bonds within a protein (intramolecular) or between two proteins (intermolecular).

What are the roles of DNA and RNA in the cell?

DNA carries heritable genetic information, while RNA is required to generate proteins from DNA information and can also function as structural and catalytic molecules.

What are the monomers of nucleic acids, and what three covalently bonded parts do they consist of?

Nucleotides, composed of a pentose sugar, a nitrogen and carbon-containing base, and a phosphate group.

What is the difference in the pentose sugar between DNA and RNA?

In DNA, the pentose is deoxyribose; in RNA, it is ribose.

Name the four different bases found in DNA.

Adenine (A), Guanine (G), Cytosine (C), and Thymine (T).

Which DNA bases are purines and which are pyrimidines?

Adenine (A) and Guanine (G) are purines (double-ring structure); Cytosine (C) and Thymine (T) are pyrimidines (single-ring structure).

How do the two strands of the DNA double helix bind together?

By non-covalent interactions, specifically hydrogen bonds between complementary bases (A-T and G-C).

How many hydrogen bonds form between Adenine and Thymine, and between Guanine and Cytosine in DNA?

Two hydrogen bonds between A and T, and three hydrogen bonds between G and C.

What are the monomers of polysaccharides?

Monosaccharides.

What is the difference between an aldose and a ketose monosaccharide?

An aldose has its carbonyl group (double bond to oxygen) at a terminal carbon, while a ketose has its carbonyl group at an internal carbon.

What type of bond connects monosaccharides to form polysaccharides?

Glycosidic bonds.

Name two common polysaccharides.

Cellulose and starch.

How are cell membranes primarily built?

By non-covalent interactions of phospholipids and other molecules.

What are the main components of a phosphoglyceride (a common phospholipid)?

Two fatty acids bound to glycerol, a phosphate group, and often a small organic 'polar group'.

What characteristic makes phospholipids amphipathic?

They have both a hydrophobic tail (fatty acid hydrocarbon chains) and a hydrophilic head (phosphate plus polar group).

How do phospholipids spontaneously arrange themselves in aqueous environments?

They self-assemble into lipid bilayers due to their amphipathic nature.

What type of bond connects fatty acids to glycerol in phospholipids?

Ester bonds.

What is the effect of unsaturated fatty acids on biomembranes?

Unsaturated fatty acids have kinks (bends) due to C=C double bonds, which prevents them from packing as tightly, thus affecting the stiffness of the membrane.