nitrogenous base

ribose

phosphate

USE

nucleotide polymers

• DNA: info storage
• RNA: gene expression

DEFINE

nitrogenous bases

• ACGT
• "coding" component of DNA cyclic compounds w/ at least 2 N atoms
• base-pair to form DNA helix

STRUCTURE

nucleotide parts

• ribose: No 2' in deoxyribose
• nitrogenous base: glycosidic bond attaches base to C1
• phosphate: attached to 5' OH

pyrimidines

purines

• single ring
• DNA: thymine & cytosine
• RNA: cytosine & uracil

• double ring
• adenine & guanine

• formed by linkage of riboses to each other via Pi
• "surface" of double helix

antiparellel to each other

5' end paired w/ 3' end

"internal"

protected by backbone

• dsDNA typicaly B-form
• Z-form: high salt conditions

• dsDNA helix wraps around to fit into cell
• important in gene regulation

A-T: 2 H-bonds

G-C: 3 H-bonds

• temperature at which DNA melts/unwinds
• dependent on sequence of base pairs and length of DNA (higher G-C content: higher Tm)

• unwinds (breaking H-bonds) creates 2 parent/conserved strands
• parent strands serve as templates for daugther strands

• point where double helix melts and semi-conservative DNA replication begins
• Ori: 2 replication forks, 1 at each end
• eukaryotic genomes: too large to have only one Ori

• origin of DNA synthesis moves away from Ori
• "bubble" around Ori lengthens

• unwind the DNA double helix
• hydrolyze ATP to provide energy for unwinding

• make transient ds breaks in DNA
• require ATP hydrolysis

• key enzyme that synthesizes DNA during replication
• catalyzes synthesis in 5' to 3'
• moves along template in 3' to 5'

ASPECTS OF

5' to 3' phosphodiester bond

• PPi (pyrophosphate released)
• makes reaciton irreversible

DEFINE

RNA primers

• required preformed primer for DNA pol for extension:  cannot initiate synthesis de novo
• generated by enzyme:  primase
• provides 3' -OH for extension by DNA pol

• easy template
• DNA primase creates 1 primer from which replication proceed continously

• difficult template
• several primers created for discontinous syntheiss of several Okazaki fragments

QUESTION

Are both synthesized DNA strands at replication fork identical?

DEFINE

polymerase

DEFINE

DNA helicase

DEFINE

primase

DEFINE

5' to 3' polymerase activity

DEFINE

5' to 3' exonuclease activity

DEFINE

3' to 5' exonuclease activity

DEFINE

telomere

• sequences at end of chromosomes
• 1000's of trandme repeast of simple G-rich sequences

PATHWAY

DNA shortening

• last primer at end of linear chromosome removed
• gap created:  no 3'-OH to extend from
• gap leads to shortening of chromosome w/ each round of replication
• eventual cell death

DEFINE

telomerase

• specialized polymerase that synthesizes telomeres
• RNA-protein complex
• reverse transciptase

DEFINE

reverse transcriptase

DEFINE

telomerase RNA

• complementary to G-rich repeat at telomeres
• base pairs w/ telomeres
• forms a primer template junction for elongation of 3' end of telomere

AFFECTS OF

telomere length regulation

• eukaryotic somatic cells:  programmed to lost telomerase activity over time
• leads to degradation of genome

DEFINE

nucleotide anolog drugs

TYPES OF

spontaneous damage in DNA

spontaneous hydrolytic attack

spontaneous oxidative damage

uncontrolled methylation

DEFINE

oxidative deamination

• results in unnatural DNA bases
• eventually leads to change in base-pair sequence

DEFINE

depurination

• glycosidic bond b/w purine base and sugar in a nucleotide will spontaneously hyudrolyze
• leaves apurinic site

EFFECT OF

UV radiation

DEFINE

pyrimidine dimer

• 2 ajacent thymine bases on same strand become linked
• creates 30 degree kink:  blocks replication and transciption

DEFINE

base-excision repair

• single damaged base recognized by specific DNA glycosylase
• cleaves bond b/w base and deoxyribose
• results in either apurinic/apyrimidinic
• AP endonuclease and phosphodiesterase remove sugar-phosphate backbone, leaving gap
• gap filled by DNA pol
• gap sealed by DNA ligase

DEFINE

nucleotide excision repair (NER)

repairs bulky adducts and damage not normally recognized by DNA glycosylases

PATHWAY

NER

1. multienzyme complex:  scans DNA for distortion of double helix
2. nuclease:  cleaves phosphodiester backbone on both sides of distortion
3. helicase:  unwinds area
4. DNA pol and DNA ligase: gap repair

DEFINE

mismatch repair

• repair base-pair mismatches missed by 3' to 5' exonuclease activity
• strand-directed:  only on newly synthesized strand

TYPES

double stranded breaks

• ionizing radiation
• oxidizing agents
• metabolic cell products
• replication errors

TYPES

double stranded break repair

nonhomologous end joining:  simplest

homologous end joining:  2nd most effective

DEFINE

nonhomologous end-joining

• broken ends juxtaposed and rejoined by ligation
• emergency solution
• can result in loss of one or more nucleotides

DEFINE

homologous end-joining