Final Flashcards
Nucleic acids
- linear polymers of nucleotides that function in the storage and expression of genetic information and its transfer from one generation to the next
Phosphodiester bonds
- link between the two monomers/nucleotides
Two Categories of Heterolytic/Nitrogenous Bases
- Purines
2. Pyrimidines
Purines
- Adenine and Guanine
- 2 fused rings: a 6 membered and 5 membered heterocyclic C and N rings fused together
Pyrimidines
- Cytosine, Thymine and Uracil
- single 6 membered heterocyclic rings of C and N
Nucleoside
- nitrogenous bases attached to sugars via Beta 1-N glycosidic bond
- rotation about glycosidic bond is possible, resulting in syn or anti configuration (anti is favored!)
- pyrimidines can’t form syn configuration because of steric hindrance
Nucleotide
Contains
- Phosphate Group
- Sugar
- Nitrogenous Base
Primary nucleotide structure
- this structure is the nucleotide sequence
- read 5’ to 3’
Secondary Nucleotide Structure
- this structure is the 3D arrangement of nucleotide residues
- short-term folding interactions
- only DNA because RNA is single stranded
Tertiary Nucleotide Structure
- this structure is the longer range 3D interactions between proteins and DNA
- superhelixes forms, cruciforms, etc.
- Sugar-phosphates form the backbone
- DNA has a “rise” one base pair to another is the rise
B-DNA
- this DNA form is seen in DNA fibers prepared under high humidity (PREDOMINANT FORM)
- double helix
- individual helixes form major and minor grooves
- right handed helix
- watson and crick described this
A-DNA
- dsRNA forms this and DNA-RNA hybrids
- right-handed helix
- shorter than B form (more compact)
- bases lie farther outside of axis
- major and minor grooves are equal in width
Z-DNA
- left handed helix
- longer than B form
- pyrimidines are anti and purines are syn
cruciform DNA
- cross-like DNA structures formed when DNA contains a PALINDROME
- palindromic sequences form a double hairpin
- involved in protein binding to DNA
- serves as recognition sites for restriction enzyme
triple helix DNA
- usually unstable DNA form
- forms from partially unwound duplex DNA under “super-helical” state
- third strand occupies major groove
- possible role in crossing over
super-coiled DNA
- DNA + protein coiled on itself several times
- functions: compacts DNA to occupy less space
- inactive (prevents replication and transcription)
- protects DNA when not replicated or transcribed
Bacterial DNA packaging
- in the NUCLEOID
- negative supercoilng and separating loops of supercoiled DNA bound to a protein to a compact genome - exists in CYTOSOL with small number of attachment points to membrane
Eukaryotic DNA packaging
- in HISTONES
- DNA is confined to nucleus and wrapped around these protein assemblies
satellite DNA
- DNA with multiple tandem repeats of short, simple nucleotide sequences
- makes up 10-20% of genome in higher eukaryotes
introns
- these repetitive sequences interrupt most eukaryotic genes
- noncoding regions
restriction-modification systems
3 types of these systems
system has 2 enzymes: DNA endonuclease and DNA methylase
1. Phage with unmodified DNA infects a bacterium with restriction systems that recognize the DNA sequence 5’GAATTC-3’
2. most phage DNA is cleaved by host restriction nuclease
3. but the few that are methylated on innermost A are protected from attack
4. phage that emerges with methylated DNA
restriction fragment length polymorphism (RFLP)
- genetic polymorphism detected by southern blotting and used to screen for genetic diseases
- based on fact that alleles often have different restriction endonuclease cleavage sites and produce different arrays of fragments upon cleavage with appropriate endonucleases
Euchromatin vs Heterochromatin
- Euchromatin- transcriptionally active
2. Heterochromatin- thicker and transcriptionally inactive
PCR (polymerase chain reaction)
- this process can exponentially make small amounts of DNA in vitro
- requires thermostable DNA polymerase (Taq pol), a pair of oligonucleotide primers that flank the region to be amplified, dNTPs, and DNA template
1. denaturing
2. annealing
3. extension
replication fork
- point of separation on dsDNA at which incorporation of nucleotides occurs during DNA replication
Semiconservative replication
- this DNA characteristic means each strand-separated polynucleotide serves as a template for synthesis of new complementary strand
semidiscontinuous replication
- this DNA characteristic means the synthesis of DNA fragments that occurs in the lagging strand during DNA replication
okazaki fragments
- discontinuous fragments of DNA synthesized in the lagging strand
Dna replication in prok
- initial unwinding, separation, and stabilization of duplex DNA (origin of rep is AT rich)
- primer synthesis
- DNA synthesis
- replace RNA primers with DNA
- ligase seals gaps between okazaki fragments
- termination of proteins
initiation factors
- DNAa proteins that bind to the origin of replication
Helicase
- DNAb proteins that catalyze ATP-dependent unwinding of duplex DNA
topoisomerase
- prevents supercoiling and tangling of DNA during unwinding
- binds ahead of fork, nicks supercoiling DNA, relaxes stress by allowing uncoiling
ssB proteins
- prevents single strands from reannealing, protect against nuclease degradation
primase
- RNA polymerase synthesizes a short (10 nucleotide) RNA primer
DNA pol I
- this polymerase fills in gaps, repairs mismatched bases, replaces primer RNA during replication
- main replicative enzyme of lagging strand
- requires template DNA and DNA or RNA primer
DNA pol II
- this polymerase is involved in some repair processes
- prevalent during stationary phase
DNA pol III
- this polymerase extends RNA-primed chain; main polymerase in elongation of leading strand
- major replicative enzyme in bacteria (beta unit, sliding clamp, etc)
telomerase
- DNA polymerase adds a short repeating segment to the 3’ end at either of chromosome DNA molecule, creating a single-stranded overhang, which gives room for priming origin of final Okazaki fragments
- advantage over PROKARYOTIC TERMINATION (they have problem completing the synthesis of the 5’ ends)
Prok termination
- Ter binding proteins bind to ter sites (20 bp inverted sequences) on opposite side of DNA loop, inhibit helices, and prevent progression of replication forks
Euk termination
- DNA pol runs off ends of DNA; replication bubbles fuse as polymerases collide; involves telomeres
Retrovirus
- possess reverse transcriptase to produce DNA from RNA template
- replicase copies the RNA viruses RNA starting form from 3’ end so the strand is laid in 5’ to 3’ direction
