EXAM 2 Flashcards
semiconservative DNA replication
during DNA replication the two strands of the parent DNA double helix separate –> each strand then forms a template for free nucleotides to bind to –> thus creating two identical daughter strands
each daughter stand winds up with a strand from the original parent and a new strand (thus, semi)
DNA polymerase
has 3’ –> 5’ exonuclease activity (known as proofreading)
proofreading
exonuclease activity used by DNA polymerase
when a wrong nucleotide is input during 5’ –> 3’ DNA synthesis, DNA polymerase can remove it using this technique in a 3’ –> 5’ fashion; the nucleotide can then be replaced, resuming 5’ –> 3’ polymerase activity
nucleotide mismatch
if left unrepaired by DNA polymerase BEFORE the next round of DNA synthesis, this action could result in permanent changes
sickle-cell anemia
consequence of a point mutation in the beta-globin gene
glutamic acid in the beta-globin protein is replaced with a valine (non-polar) due to a single nucleotide substitution in the DNA
nicks
breaks in recently synthesized stands
Okazaki fragments
short fragments due to the discontinuous synthesis of the lagging strand during DNA replication
these fragments polymerize 5’ –> 3’ and need to be amended via nick repair
DNA mismatch repair proteins
(in eukaryotes)
these proteins recognize a mismatched pair because of the topological disturbance and take the change to bind to it
mismatch repair
(in eukaryotes)
1) DNA mismatch repair proteins recognize the mismatch pair and bind to it
2) the DNA is scanned for any nicks in the DNA
3) the nicked strand is digested all the way from the nick back to the mismatch site
4) DNA polymerase and DNA ligase complete the rapair
cytosine deamination
a deaminated C is a mismatch in which G is paired with a U (C–>U)
after DNA replication, one strand will be mutated & contains the U that will code for an A (G–>A)
the G containing strand of the parent will go unchanged
main point: cytosine pairs with guanine and uracil pairs with adenine
adenine deamination
main point: adenine pairs with thymine and hypoxanthine pairs with cytosine
depurination
results in a depurated sugar and no base pairing
a depurinated A in the parent strand has no A paired with the respective T
after DNA replication, the mutated strand is distorted by deletion of the A-T nucleotide pair
the new strand with the parent strand containing the T will go unchanged after DNA replication
direct reversal (direct repair)
a general category of repair mechanisms for spontaneous mutations
this action fixes the altered molecular by reversing the chemical transformation occurring
it requires specific enzymes for each individual lesion (i.e. some organisms reverse thymine dimers by using a specific photo reactivating enzyme)
base excision repair
is a general mechanism for repairing nucleotide mismatches caused by spontaneous mutations
chemical transformation is not reversed, but the damaged base(s) are replaced instead
the unpaired base is recognized and replaced before DNA replication occurs
spontaneous mutation
these mutations introduce things that don’t belong in the DNA and are easily recognizable by the cell for repair
base excision repair mechanism
1) DNA glycosylase removes the damaged base leaving only the sugar and phosphate backbone to remain); an endonuclease recognizes the site and cleaves the phosphodiester bond; a deozyribosephosphodiesterase removes the remaining sugar and phosphate
2) DNA polymerase places a new nucleotide (5’–>3’)
3) DNA ligase seals the nick (3’–>5’?)
DNA rearrangements
recombination events that alter the arrangement of genes within the genome
site-specific recombination
occurs between specific DNA sequences that share partial sequence homology (similarity)
this rearrangement doesn’t depend on DNA sequence recognition between chromosomes but instead, specific proteins recognize the homologous sequences and mediate somatic recombination
lytic lifestyle
free circular DNA in host bacterial cell
immunoglobulins
antibodies
bacteriophage (phage)
a virus that infects bacteria
lysogenic lifestyle
linear DNA integrated in host DNA (a prophage)
attP (phage)
(before insertion) a common core sequence (O) is flanked by two gamma-specific sequences (P and P’)
P-O-P’
after insertion attL: B-O-P’
attachment sites
include the attP site in phage DNA and the attB site in the host bacterial DNA
insertion resulting in two new sites attL and attR
attB (bacteria)
(before insertion) same common core sequence (O) flanked by two bacterial specific sequences (B and B’)
B-O-B’
after insertion attR: P-O-B’
transposable element
chromosome segment that can move
insertion sequences
simple bacterial transposons
non replicative transposition
“cut and paste”
the insertion sequence is cut from the donor site and pasted into the target site, resulting in the insertion sequence moving from one site of the genome to another
replicative translation
“copy and paste”
a copy of the insertion sequence is made by local DNA replication and pasted into the target site, resulting in a new copy of the insertion sequence appearing at the target site
retrotransposition
requires the synthesis of a copy of a retrotransposon that is catalyzed by the enzyme reverse transcriptase
multipotent
stem cells that have the ability to differentiate into all cell types within one particular lineage (think of blood stem cells)
pluripotent
cells that can become ANY cell in the entire body
epigenetics
the study of changes and variations in phenotypes that are potentially heritable, but are not caused by permanent changes in DNA base sequences
transcription regulatory proteins
function is to activate the transcription of DNA by binding to specific DNA sequences
transcription initiation complex
formed by transcription regulators, general transcription factors, and RNA polymerase
MyoD
a single transcription regulator that commits cells to become myoblasts (muscle cell precursors that then form into multinucleate myotubes that become muscle fibers)
*** the combinatorial control of the muscle cell fate
induced pluripotent stem cells (iPS cells)
in the case of mice, cultured fibroblasts can be programmed to become these types of cells by the artificial expression of three transcription regulators (oct4, Sox2, klf4)
epimorphic regeneration
(in salamanders)
adult cells dedifferentiation becoming neoblasts that undergo rapid cell division and become re-specified to form the missing adult structure
epigenetic inheritance
involve heritable changes in gene expression that are not caused by changes in the DNA sequence
examples:
1) feedback loop circuits involving transcription regulators
2) preservation of covalent histone modifications and chromatin condensation patterns
3) preservation of DNA methylation patterns
nucleosome core particle
a cluster of 8 histone proteins
histone modifying enzyme
is preserved throughout the cell division and passed on to daughter cells
DNA methylation
may occur on CG sequences and only at specific sites depending on the needs of the cell in relation to gene expression
these methylated sites turn OFF gene expression by attracting proteins that block transcription
maintenance methyltransferase
an enzyme that recognizes only already methylated CG sequences and catalyzes the methylation of the corresponding Cis in the new, complementary strand
this enzyme is preserved through division and passed onto daughter cells to preserve the pattern
de novo methyltransferases
establish new DNA methylation patterns during development or in response to external cues such as the environment, behavior, or diet
