BIOL 4087 : Class Notes For Exam 2
BioChem Exam 2 – 1
Chapter 8 and chapter 25
Nucleotides
DNA metabolism
Nucleotide structures
Phosphodiester bond
Structure of DNA – double stranded helix
DNA replication
DNA repair
DNA sequence
Central dogma: DNA → transcription → RNA → translation → protein
DNA → DNA replication → DNA
Nucleic acids: DNA and RNA
o
o KNOW NAME AND STRUCTURE OF BASES!!!
o Nucleoside – base + sugar (no phosphate)
▪ adenosine
▪ guanosine
▪ cytidine
▪ uridine
▪ thymine or 2’-deoxythymine
o nucleotide – sugar + base + phosphate
▪ adenosine 5’ monophosphate, adenylate, AMP
▪ guanosine 5’monophosphate, guanylate, GMP
▪ 2’-deoxycytidine 5’ monophosphate, deoxycytidylate
▪ 2’-deoxythymidine 5’monophophate, deoxythymidylate, dTMP
▪ Uridine-5’-monophosphate, uridylate, UMP
BioChem Exam 2 – 2
▪ KNOW NAMES AND STRUCTURE!!!
▪ Azidothymidine (AZT) – HIV reverse transcriptase inhibitor
• RNA → DNA
•
• Figure 8-6
o Phosphodiester linkage – join nucleotides together
▪ Figure 8-7
▪ Could write out as 5’ pApTpG 3’ or ATG
▪ Write with 5’ on left and 3’ on right
o Watson and Crick discovered the structure of DNA from Franklin and Wilkins
BioChem Exam 2 – 3
▪ Figure 8-11
▪ Figure 8-13 – Major and minor grooves
▪ 1. Double stranded
▪ 2. Chains run in opposite direction (antiparallel) and they are complementary to
each other
▪ 3. Hydrogen bonding between bases
• AT → 2 hydrogen bonds
• GC → 3 hydrogen bonds
• Holds DNA together w/ lots of H-bonds but the individual bonds are
weak, allowing proteins to pull the strands apart
▪ 4. DNA forms double helix with bases on inside while sugar + phosphate are on
the outside
▪ 5. Major and minor grooves where bases interact with protein
o 3 forms of DNA
▪ Figure 8-17
▪ B form – classic double stranded DNA
▪ A form – RNA/DNA hybrid and dsRNA
▪ Know these, and know that double stranded DNA is B form
o Denaturation
▪ Figure 8-26
▪ Figure 8-27a – GC base pairs denature at a slightly higher temperature than AT
b/c extra H-bond
▪ dsDNA → heat → ssDNA
▪ ssDNA → cool →dsDNA
▪ measure DNA denaturation by measuring absorption at 260 nm
o DNA replication
▪ Figure 8-15
▪ Semi-conservative – on parent strand is found in each of the daughter strands
▪ Figure 25-1 oriC and Ter sequences on opposite sides of chromosome
▪ Figure 25-3
▪ Figure 25-4 – know!
▪ DNA replication is bidirectional – replication forks move in different direction
▪ 5’ to 3’ synthesis of new DNA strand
• leading strand: continuous synth
• lagging strand: Okazaki fragments
o DNA polymerase
▪ Deoxynucleosidetriphophate (dNTP)
• E.g. dATP, dGTP, dTTP, dCTP
▪ (DNA)n + dNTP → (DNA)n+1 + PPi KNOW THIS RXN
▪ PPi = pyrophosphate
• PPi → 2Pi
Document Summary
Structure of dna double stranded helix. Central dogma: dna transcription rna translation protein. Biochem exam 2 2: know names and structure!! Biochem exam 2 3: figure 8-11, figure 8-13 major and minor grooves, 1. Chains run in opposite direction (antiparallel) and they are complementary to each other: 3. Hydrogen bonding between bases: at 2 hydrogen bonds, gc 3 hydrogen bonds, holds dna together w/ lots of h-bonds but the individual bonds are weak, allowing proteins to pull the strands apart, 4. Dna forms double helix with bases on inside while sugar + phosphate are on the outside: 5. See figure 8-9: dna polymerase iii, fig 25-9, synthesizes most of dna, alpha subunit carries out 5" 3" synthesis (polymerase, epsilon subunit carries out 3" 5" proofreading (exonuclease, bata subunit is the clamp (beta clamp) Clamp loading complex": high processivity: remains bound for more than 500,000 bases, processivity number of nucleotides added before polymerase dissociates.
