Biological Molecules Part II: Proteins and Nucleic Acids

Comprehensive review flashcards covering biological molecules including protein structures and functions, nucleic acid chemistry, DNA/RNA organization, and comparative biochemistry of macromolecules.

What percentage of the dry mass of most cells is accounted for by proteins?

More than $50\%$ of the dry mass of most cells.

What is the biological definition of a protein?

A biologically functional molecule made up of one or more polypeptides, each folded and coiled into a specific 3D structure.

What are the seven dynamic functions of proteins highlighted in the lecture?

$1.$ Speeding up reactions (catalysts) $2.$ Storage $3.$ Cellular communication $4.$ Structural support $5.$ Defense $6.$ Transport $7.$ Movement

What is the function of enzymatic proteins, and what is an example provided in the lecture?

Selective acceleration of chemical reactions; for example, digestive enzymes catalyze the hydrolysis of bonds in food molecules.

What is the function of transport proteins, and how does hemoglobin fulfill this role?

Transport of substances; hemoglobin is the iron-containing protein of vertebrate blood that transports oxygen from the lungs to other parts of the body.

What general monomer structure is shown in this diagram, and how many distinct types are utilized in polypeptides?

An amino acid monomer; there are $20$ distinct types joined by peptide bonds.

What component of an amino acid determines its unique physical and chemical characteristics?

The side chain ($\text{R}$ group).

What are the primary chemical composition and water affinity of nonpolar amino acid side chains?

They are composed primarily of carbon and hydrogen, making them hydrophobic.

Which amino acids possess acidic (negatively charged) side chains, and which possess basic (positively charged) side chains?

Acidic: Aspartic acid ($\text{Asp}$ or $\text{D}$) and Glutamic acid ($\text{Glu}$ or $\text{E}$). Basic: Lysine ($\text{Lys}$ or $\text{K}$), Arginine ($\text{Arg}$ or $\text{R}$), and Histidine ($\text{His}$ or $\text{H}$).

How does a peptide bond form, and what are the two distinct ends of a polypeptide chain?

It forms via a covalent dehydration reaction; the two ends are the $\text{N-terminus}$ (free amino group) and the $\text{C-terminus}$ (free carboxyl group).

What are the four recognized levels of protein structure?

Primary, Secondary, Tertiary, and Quaternary structure.

What constitutes the primary structure of a protein?

The precise linear sequence of amino acids.

What two secondary protein structure conformations are shown here, and what type of bond stabilizes them?

$\alpha$ helix and $\beta$ pleated sheet; both are stabilized by hydrogen bonds along the polypeptide backbone.

How is an $\alpha$ helix coil specifically held together in a secondary structure?

By hydrogen bonds between every $4^{\text{th}}$ amino acid.

What defines the tertiary structure of a protein?

The overall shape of a polypeptide resulting from interactions between the $\text{R}$ groups (side chains) of amino acids.

Which tertiary interaction depicted in this diagram is a covalent bond formed between two sulfhydryl groups?

Disulfide bridge.

What fibrous protein structure is shown here, consisting of three identical helical polypeptides intertwined into a triple helix?

Collagen (which makes up $40\%$ of protein in the human body).

What is the quaternary structure of hemoglobin?

A globular protein consisting of four polypeptide subunits ($2\,\alpha$ and $2\,\beta$ subunits), each containing a nonpolypeptide iron-containing heme group.

Based on this comparison, what specific amino acid change in the primary structure of the $\beta$ subunit causes sickle-cell anemia?

The replacement of glutamic acid ($\text{Glu}$) at position $6$ with valine ($\text{Val}$).

What is protein denaturation, and what environmental factors can trigger it?

When a protein unravels and loses its native shape due to the weakening of chemical bonds; it depends on factors such as $\text{pH}$, salt concentration, and temperature.

Which human diseases are cited in the lecture as originating from protein misfolding?

Cystic fibrosis, Alzheimer’s disease, Parkinson’s disease, and mad cow disease.

What is unique about DNA compared to other biological molecules?

DNA provides directions for its own replication.

What is gene expression according to the lecture?

The process where DNA directs RNA synthesis and, through RNA, controls protein synthesis.

What three components comprise a nucleotide monomer?

$1.$ Nitrogenous base $2.$ Five-carbon sugar (pentose) $3.$ Phosphate group

What is the structural difference between pyrimidines and purines?

Pyrimidines have one six-membered ring of carbon and nitrogen atoms; purines have a six-membered ring fused to a five-membered ring of carbon and nitrogen atoms.

Which nitrogenous bases belong to the pyrimidines, and which belong to the purines?

Pyrimidines: Cytosine ($\text{C}$), Thymine ($\text{T}$), and Uracil ($\text{U}$). Purines: Adenine ($\text{A}$) and Guanine ($\text{G}$).

Which nitrogenous base is exclusive to DNA, and which is exclusive to RNA?

Thymine ($\text{T}$) is found only in DNA; Uracil ($\text{U}$) is found only in RNA.

What sugar is found in DNA nucleotides, and what sugar is found in RNA nucleotides?

Deoxyribose in DNA; ribose in RNA.

How do base-pairing rules differ between DNA and RNA?

In DNA: $\text{A}$ pairs with $\text{T}$, and $\text{G}$ pairs with $\text{C}$. In RNA: $\text{A}$ pairs with $\text{U}$, and $\text{G}$ pairs with $\text{C}$.

Which of the four major classes of biological molecules are polymers, and which class is neither a polymer nor a macromolecule?

Carbohydrates, proteins, and nucleic acids are polymers and macromolecules; lipids are neither polymers nor macromolecules.

What are the chemical components and main function of triacylglycerols?

Glycerol combined with three fatty acids; they serve as an important energy source.

What components make up a phospholipid, and what structure do they assemble into in aqueous solutions?

Glycerol, a phosphate group, and two fatty acids; they assemble into the lipid bilayers of cell membranes.

What is the structural characteristic of steroids, and what are two primary examples?

Four fused carbon rings with attached chemical groups; examples include cholesterol (cell membrane component) and hormones (signaling molecules).

Which polysaccharides store glucose for energy in plants versus animals?

Starch in plants; glycogen in animals.

Which polysaccharides serve structural support roles in plants versus animals and fungi?

Cellulose strengthens plant cell walls; chitin strengthens animal exoskeletons and fungal cell walls.