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Prokaryote
- no membrane enclosed organelle
- chromatin contained in nucleoid
Eukaryote
- nuclear membrane and membrane bound organelle or vesicles
Genome
Total genetic information of an organism
chromosome
independent domains of genetic information
- condensed chromatin for cell division
- each contains a centromer - site of attachment to mitotic spindle)
- ends are telomeres
genes
segments of DNA transcribed into RNA
Non-coding DNA
Control sequences that regulate expression of genes + unknown function
Transformation
introduction of novel biological information through gene transfer
Nucleic Acids
bases, sugars, and phophates
purines
adenine and guanine (double rings)
Pyrimidines
cytosine, thymine, uracil (RNA only)
single ring
Nucleoside
purine/pyrimidine bases + pentose (ribose or deoxyribose)
Nucleotide
phosphorylated nucleosides
- AMP, ADP, ATP (5' OH)
Polynucleotide
long polymers of nucleotides
- DNA with 3'-5' phosphodiester bonds
Oligonucleotide
short polymers of nucleotides (<30)
Interactions between bases of double helix
Hydrogen bonds
Hydrogen bonds between base pairs
AT - 2 hydrogen bonds
GC - 3 hydrogen bonds - more stable
Shielding
Mg2+ cations shield negative charged phosphate groups (which make DNA acidic)
DNA ligase
forms phosphodiester bond between 5' and 3' ends
Circular DNA
- bacteria, plasmids, mitochondria
- protection from degradation by exonuclease
Enzyme
substrate binding site - specificity
enzymatic site - act on substrate
exonucleases
cleave nucleotides residue at either end
endonuclease
cleave phophodiester bond interior of polynucleotide
Forms of DNA
A DNA - DNA-RNA hybrid during transcription
B DNA - primarily in cless
Z DNA - DNA sequences that control gene transcription
denaturation
separation of two strands during replication and transcription
"Open-stranded bubbles"
Form usually at AT, reanneal, release free energy and move down DNA strand
Topoisomerases
- regulate supercoiling
- caatlyze breaking and rejoining of DNA strands
- Type I - only break 1 strand and allow to rotate
- Type II - break both DNA strands, relax supercoil (requires ATP) (inhibited by novobiocin)
Gyrase
topoisomerase that relieves supercoiling by unwinding DNA
- inhibited by Nalidixic acid
Cruciform DNA
intrachain bond forms - function to control replication and transcription
Triplex DNA
- string of purine bases needed
- functions in transcription control initiation and termination of replication and enhance stability
- hydrogen bonding in major groove
- Hoogsteen pairing of bases
- no triple helix - still produce fetal hemoglobin
Quadruplex DNA
- immunoglobin genes that undergo recombination
- telomeres
Histones
basic proteins that bind DNA in eukaryotes
- 8 proteins form histone disk
- interact with minor groove
H1- does not form part of disk, but stabilizes DNA
HU proteins
- protein that prokaryote DNA associates with - pack into nucleoids

Nucleosomes
DNA with histone disk
- DNA between nucleasomes - linker DNA
- linear arrays are nucleofilaments, which make DNA fibers, which make chromosomes
Chromatosomes
DNA with histone disk and H1
Chromatin
DNA with associated proteins
- euchromatin and heterochromatin
Special DNA sequences
inverted repeat (palindrome) - self-complementary with symmetry elements
mirror repeat - identical base pairs equidistant
direct repeat - particular sequences repeated in one strand
structural genes
DNA coding sequences for proteins
- eukaryotic cells - no overlap like prokaryotic cells
Introns
parts of eukaryotic genes that are spliced out to leave only exons
DNA Replication requires:
template, primer, nucleotides, DNA polymerases
primer
short segments of RNA that are synethized by primase hydrogen bonded to the template
- provides free 3' OH groups to add nucleotides
Reaction to add nucleotide
pyrophosphate, PPi, is released
Single stranded DNA binding proteins (SSB)
keep DNA from reannealing during replication (prokaryotes)
Klenow fragment
part of DNA polymerase Pol I
- used for primer removal (5'->3' exonuclease)
Processivity (Prokaryotes and Eukaryotes)
- ability of an enzyme to stay on the substrate during synthesis
- Prokaryotes: Pol III has higher processivity than Pol I or Pol II -->sliding clamp
- Eukaryotes - Polymerase δ higher processivity than Polymerase α k -->proliferating cell nuclear antigen (PCNA)
Origin of Replication (Ori)
- point at which replication begins
- where DNA ligases, polymerases, primases bind
primosome - Ori+ptns for synthesis
replisome - Ori+ptns for replication (OriC)
replicons
- segments of DNA between Ori's
cyclin dependent kinases
- control cell cycle by acting on cyclin
- initiates cell div/cell replication during S phase
replication protein A (RPA)
- keeps DNA from reannealing during DNA replication (eukaryotes)
reverse transcriptases
- use an RNA template for DNA synthesis
- e.g. viruses and telomerase
- lacks 3'->5' exonuclease activity - errors!
AZT
- treatment for AIDS - replaces dTTP with AZT which stops replication because does not have a 3' OH site
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