Lecture 1/15/25 Flashcards
Why are hydrophobic interactions significant for protein folding?
They drive protein folding by causing nonpolar residues to cluster inside, stabilizing structure.
How about covalent bonds, ionic bonds, or van der Waals interactions?
Covalent bonds stabilize backbone; ionic bonds contribute to structure; van der Waals interactions help packing.
What are the R groups of amino acids?
Side chains that define amino acid properties (polar, nonpolar, acidic, basic).
Which R groups (hydrophilic or hydrophobic) are found on the protein surface?
Hydrophilic R groups are found on the surface; hydrophobic R groups are buried inside.
What R groups are in transmembrane domains or exposed to extracellular environments?
Hydrophobic R groups interact with phospholipid tails; hydrophilic R groups face extracellular space.
Why are van der Waals interactions and hydrogen bonds significant for DNA structure?
They stabilize base pairing and stacking, maintaining the double helix.
What components make up a DNA nucleotide?
A phosphate group, a deoxyribose sugar, and a nitrogenous base.
What is the difference between DNA and RNA nucleotides?
DNA has deoxyribose and thymine; RNA has ribose and uracil.
Which components make up the DNA backbone?
Phosphate and sugar form the backbone; phosphodiester bonds hold it together.
What do the terms 5’ and 3’ refer to?
They refer to carbon positions in the sugar; 5’ has a phosphate, 3’ has a hydroxyl.
Where are 5’ and 3’ ends found on dsDNA?
5’ and 3’ ends are opposite on each strand in an antiparallel orientation.
Why does DNA need to be compacted?
To fit within the nucleus and regulate gene expression.
How is DNA compaction achieved?
DNA wraps around histones, forming nucleosomes and higher-order structures.
What are the structural differences among bases, nucleosides, and nucleotides?
Bases are nitrogenous molecules; nucleosides are bases with sugars; nucleotides have phosphate groups.
What is a dNTP?
A deoxyribonucleotide triphosphate, a building block for DNA replication.
