Chapter 6 Flashcards
Nucleosides
- Composed of a 5 carbon sugar (pentose) bound to a nitrogenous base
- Formed by covalently linking base to C1 of the sugar
Nucleotides
- Formed when one or more phosphate groups are attached to C5 of a nucleoside
- Often named by the number of phosphates bound
- High-energy compounds because of teh energy associated with the repulsion between closely associated negative charges on the phosphate groups
- Nucleotides are the building blocks of DNA
Backbone of DNA
- Alternating sugar and phosphate groups
- Always read 5’ to 3’
-Formed as nucleotides are joined by 3’ to 5’ phosphodiester bonds
Purines
- Contain two rings
- Adenine and guanine
Pyrimidines
- Contain only one ring
- Cytosine, thymine and uracil
-Thymine is only found in DNA and Uracil is only found in RNA
Watson-Crick model
- Two strands of DNA are antiparallel (oriented in opposite directions)
- Sugar phosphate backbone is on the outside (hydrophilic) of the helix with nitrogenous bases on the inside (hydrophobic)
- A with T (2 H bonds) and G with C (3 H bonds) thus C/G is a stronger bond
Chargaff’s Rules
The total amount of purines will be equal to the total pyrimidines overall
B-DNA
- Right-handed helix
- Makes a turn every 3.4 nm and contains 10 bases within that span
Denaturation
- Conditions that disrupt h bonds and base-pairing
- “melting” of the double helix into two single strands (none of the nucleotides in the backbone break)
-Heat, alkaline pH and chemicals like formaldehyde/urea are most commonly used
Reannealing
- DNA can be brought back together if the denaturing condition is slowly removed
- Important step in laboratory processes like polymerase chain reactions (PCR)
DNA Replication- Heterochromatin and euchromatin
- During the S phase of interphase
- Small percentage of chromatin remains compacted during interphase and is referred to as heterochromatin (Transcriptionally silent)
-Dispersed chromatin is euchromatin- contains genetically active DNA
Telomere
- Repeating unit TTAGGG at the end of DNA
- Some lost in each round of replication but can be replaced by the enzyme telomerase
- Progressive shortening of telomeres contributes to aging
- High GC content creates strong strand attractions at the end of chromosomes to prevent unraveling
- Think of telomeres as “knotting off” the end of the chromosome
Centromeres
- Found at the center of chromosomes
- Composed of heterochromatin- which is composed of tandem repeat sequences that contain high GC content (why microtubules have to separate the chromatids during anaphase)
Replisome/Replication Complex
Set of specialized proteins that assist the DNA polymerases
Origins of replication
- Where DNA begins unwinding (Where replication begins)
- Generation of new DNA proceeds in both directions- creating replication forks
Helicase
-Enzyme responsible for unwinding DNA, generating two single stranded template strands ahead of the polymerase
Nucleases
Degrade DNA
DNA gyrase/DNA topoisomerase II
introduces negative supercoils by working ahead of helicase, nicking both strands, passing dna through the strands and releasing it
DNA polymerase
- Responsible for reading the DNA template (parent strand) and synthesizing the new daughter strand
- Reads template 3’ to 5’ while synthesizing in the 5’ to 3’ direction
DNA Ligase
- Closes the gaps between Okazaki fragments
- Lacks proofreading ability so likelihood of mutations in lagging strand is considerably higher
Single Stranded DNA binding proteins
Bind to unraveled DNA strands, preventing both the reassociation of the strands and degradation by nucleases
Supercoiling
- Wrapping of DNA on itself (as its helical structure is pushed further toward the telomeres during replication
- Picture telephone cord wrapping on itself
DNA gyrase/DNA topoisomerase II
introduces negative supercoils to reduce the risk of strand breakage
Leading strand
- strand that is copied in a continuous fashion, same direction as the replication fork
- read 3’ to 5’ and replicated 5’ to 3’
Primase
- Synthesizes RNA primer that is laid down to start DNA replication
- RNA primers are constantly added to lagging strands because each Okazaki fragment must start with a new primer
DNA polymerase III (prok) & DNA polymerases alpha and delta (euk)
Synthesize daughter strand in 5’ to 3’ manner
DNA polymerase I (prok) & RNase H (euk)
Remove RNA primer
DNA polymerase I (prok) & DNA polymerase delta (euk)
Add DNA nucleotides where RNA primer had been
Methylation
Parent strand has been around longer so it is more methylated than the daughter strand.
-also plays a role in transcriptional activity of DNA
Metastasis
Migration to distant tissues by the bloodstream or lymphatic system
Cancer cells
Proliferate excessively b/c they are able to divide without stimulation from other cells
-Over time cancer cells tend to accumulate mutations
Oncogenes
Mutated genes that cause cancer
-encode cell cycle related proteins
Proto-oncogenes
oncogenes that are not yet mutated
Tumor suppressor genes
Genes like p53 or Rb
-encode proteins that inhibit the cell cycle
-normally function to stop tumor progression and can be called antiongogenes
Mismatch Repair
-Machinery in the G2 phase (encoded by MSH2 and MLH1 which detect and remove errors introduced in replication that were missed during the S phase)
Nucleotide Excision Repair
Thymine dimers (induced by ultraviolet light) that interfere with DNA replication are removed from DNA -Recognized by bulge in the strand
-Excision endonuclease nicks the phosphodiester backbone of damaged strand and removes defective oligonucleotide
Base Excision Repair
- Uracil found in DNA
- Affected base is recognized and removed by a glycosylase enzyme- leaving an AP site
-AP site recognized by an AP endonuclease that removes damage sequence
Palindromic
The 5’ to 3’ sequence of one strand is identical to the 5’ to 3’ sequence of the other in antiparallel orientation
Restriction enzymes/restriction endonucleases
- Enzymes that recognize specific double stranded DNA sequences
- Isolated from bacteria, their natural source
-Some produce offset cuts, yielding sticky ends on framents
DNA libraries
-Large collections of known DNA sequences- these sequences could equate to the genome of an orangism
Hybridization
The joining of complementary base pair sequences
-Uses two single stranded sequences and is a vital part of PCR and southern blotting
-Can be DNA-DNA recognition or DNA-RNA recognition
Southern Blot
Used to detect the presence and quantity of various DNA strands in a sample
-DNA cut by restriction enzymes and then separated by gel electrophoresis.
