Biochemistry Exam 3

• Nucleotides have a phosphate group, a nitrogenous base, and a pentose sugar
• ribose has a hydroxyl group on the 2' carbon
• deoxyribose has a hydrogen on the 2' carbon
• the nitrogenous base makes a glycosidic bond with the anomeric carbon
• Ribose is a B-furanose
• Cytesine, thymine, and uracil are all pyrimidines
• guanine and adenine are purines
• DNA uses thymine due to the possibility of deamination
• Nucleotide polymers are made by phosphodiester linkages
• When C&G are found in higher amounts, it is harder to separate the DNA strands
• A and T have two bonds between them
• C and G have three bonds between then
• Van der Waals interactions occur between stacked bases
• Bases of a base pair are not perfectly coplanar
• the B-form of DNA is the most common
• in DNA strands, hydrogen bonds occur between bases and phosphodiester bonds connect the back bone
• relaxed DNA does not move as far in gels as supercoiled DNA
• DNA absorbs best at 260 nanometers
• DNA replication begins at the origin of replication
• At the site of replication, the helix is unwound, which creates a replication fork
• replication is bidirectional, so there are two replication forks
• bacteria only have one origin of replication
• DNA polymerase requires a DNA template and 4 deoxyribonucleotide phosphates (dNTPs)
• Chain elongation occurs in the 5'-3' direction, with a nucleotide being added to the 3'-OH
• All 3 nucleases have 3'-5' exonuclease activity, in which they excise primers and fill in the gaps left behind
• Polymerase I is the only polymerase with exonuclease activity in the 5'-3' direction
• Holoenzymes contain core enzyme complexes made up of subunits, each providing a different catalytic function
• dnaA is the gene responsible for the unwinding of the double helix
• DNA helicase is a hexamer of subunits and is made up of dnaB polypeptides
• helicases require energy supplied by hydrolysis of ATP, a process that denatures the hydrogen bonds and destabilizes the double helix
• DNA gyrase is a specialized topoisomerase
• primase is recruited to the replication fork by helicase
• the two strands of the double helix are antiparallel
• Eukaryotic replication is different because chromosomes are linear, they have multiple chromosomes, histones, and utilize more polymerases
• Forms of metagenesis include deamination, thymine dimers, depurination, and guanine tautomers
• EMS is how mutations are purposefully made in lab
• methylation is used after replication to distinguish old and new strands
• double stranded breaks can cause chromosomal rearrangement, cancer, or cell death
• E.coli RNA polymerase has an additional unit called a sigma factor
• transcription results in ssRNA