ch 6- molecular genetics Flashcards
diff between RNA and DNA
RNA- 2 OHs
DNA- only one OH on the 3’
in DNA with higher proportion of G-C bonds,
higher temperature is needed to break apart the strands
how many origins of replication are there
circular DNA- only one
linear DNA- multiple
semi conservative meaning
each new strand of DNA has one old strand and one new
5’ and 3’ end of DNA
5’ - phosphate
3’ - hydroxyl
what is the initiation step of DNA replication
- origin of replication created at AT rich segments using helicase - replication fork created which leads to supercoiling up ahead
single strand binding protein
bind to uncoiled DNA during ELONGATION to prevent it from reattaching
topoisomerase
nicks DNA double helix ahead to relieve build up tension and supercoiling
also called DNA gyrase
primase
places RNA primers at the origin of replication
creates 3’ end
sliding clamp proteins
holds DNA polymerase to the template strand
leading vs lagging strand
leading- produced continuously bc it has a 3’ end that faces the repliaction fork
laggin strand- produced discontinously bc its 3’ end is facing away from the replication fork
- needs many RNA primers to produce okazaki fragments
what happens to the rNA primers
replaced by another DNA polymerase with DNA
DNA ligase
glues separated fragments of DNA together
telomeres
non coding repeated nucleotide sequences at the ends of linear chromosomes
important in euk bc when the replication fork reaches the end of a chromosome, a small segment of DNA from the telomere is not replicated and lost (no RNA primer is present to help produce another Okazaki fragment).
telomerase
enzyme that extends telomeres to prevent DNA loss (adds repeatitive DNA)
DNA polymerrase
class of enzymes that extends DNA from the 5’ to 3’ direction
some have proofreading abilities
nucleosomes
DNA complexes wrapped around histone proteins
histones
positively charged
negatively charged DNA wraps around them
euchromatin vs heterochromatin
euchromatin- loosely packed nucleosomes - DNA accesible for transcription
heterochromatin- tightly bound chromatin so DNA is mostly inactive
acetylation
removing positive charges of DNA relaxing the nucleosomes
- ALLOWS MORE TRANSCRIPTION TO OCCUR
deacetylation
increases positive charge- more tight binding of histones to DNA
decreases transcription
methylation
adds methyl groups
can either increase or decrease transcription
steps of transcription
initiation- promoter attracts RNA polymerase to gene
elongation- transcription bubble is formed- RNA pol travels 3’ to 5’ direction on the template strand extending rNA in 5’ to 3’ direction
temination- termination sequence signals RNA pol to stop transcribing
another name for template strand
antisense
noncoding
what is the coding/ sense strand
it isnt the template
it will have a sequence that is nearly identical to DNA but the T will be U
R factor
extra chromosomal peices of DNA that form plastids
contain ANTIBIOTIC RESISTANCE GENES
transduction
transfer of DNA between bacteria through viruses
occurs when virus enters lysogenic cycle- carriers bact dna with its own when it goes back to lytic cycle
transformation
bact take up extracellular DNA
bact that can do that are called competent
how to make bact competent
electoporation
conjugation
bac use cytoplasmic bridge- pili to copy and transfer the F plasmid (F+) if it doesnt have this it is F-
how do bacteria increase genetic diversity
through horizontal gene transfer
conjugation
tranformation
transduction
prohpages
bacteriophage genome that has been integrated into the host genome
what is the viral replication cycle
attachment-
penetration
uncoating- viral capsid removed and degraded by host enzymes
replication
assembly - viral capsid components assemble to form the viral capsid
release
why are viruses not living
because they must infect livinh cells to multiply
capsid
viral protein that is made of capsomere subunitsl
lysogenic cycle
visu considred dormant
inserts its own genome into host genome
does not harm host
lytic cycle
virus takes over host to replicate and does cayse harm
retrovirus example
HIV
retroviruses
Retroviruses (e.g., HIV) have an RNA genome that infects host cells. They contain an enzyme called reverse transcriptase, which converts their RNA into cDNA (complementary DNA). The cDNA can integrate into the host genome and enter the lysogenic cycle.
operon
group of gnees that functions as a single unit controlled by one promoter
how are operons promoters regulated
repressors or activators bind
what kind of operon is the lac operon
inducible operon
contains lac Z, Y, A
encodes lactose metabolism
only induced when glucose not available
how is the lac prootein regulated - first
the lac repressor protein - constituitively expressed- always turning off the lac protein expression
when lactose is present - converted to allolactose which binds to the REPRESSOR and prevents it binding to operator
how is the lac operon regulated- second
CAMP- inversely related to glucose. high when glucose is low
it binds to CAP- binds near lac operon promoter attracting RNA polymerase
what happens when lactose is present and glucose is present
moderate transcription of the lac operon
repressor not bound
CAP not bound
what does CAP stand for
catabolite activator protein
what happens when lactose is present and glucose is absent
high transcription of lac operon
repressor not bound
CAP bound
what happens when lactose is absent and glucose is present
no transcription of lac operon
repressor is bound and CAP is not bound
when happens when both lactose and glucose are absent
no transcriptino of lac operon
repressor is bound and CAP is bound
what is the trp operon
responsible for producing the tryptophan amino acid
its repressible - encodes for tryptophan synthetase and always active unless trp is present in enviroment
how is the trp operon regulated
trp binds to the trp repressor protein which attaches to teh operator
what RNA pol is used by eyk
RNA pol II
what do transcription factors do
needed in EUK to help RNA pol to bind to promoter
TFs bind to the TATA box in promoters
enhancers
DNA sites that activator proteins bind to to inc transcription
silencers
DNA sites that repressor proteins bind to to decrease transcription of a gene
where are enhancers and silences
far upstream or downstream so DNA probably loops around to colocalize with RNA polymerase
where is the poly A signal found
within the terminator
stimulates polyadenylation - addition of adenine nucleotides to the 3’ end of mRNA
conversion of premRNA to processed mRNA
occurs after post transcriptional modification
processed mRNA leaves the nucleus
post transcriptional modification
5’ capping - 7 methylguanosine cap added to 5’ end DURING ELONGATION
polyadenylation of 3’ end
splicing out introns- using spliceosomes (signalled by splice signals)
what is the benifit of 5’ cap
prevent degradation
benifit of polyadenylation
prevent degradation
how many protein coding genes do we have
20,000
more non coding DNA than coding
miRNA
(micro RNA) are small RNA molecules that
silence mRNA expression as a method of
post-transcriptional gene regulation by base-pairing with parts of sequences on the mRNA transcript that inhibits their translation.
snRNA
make the functinal part of the spliceos0me
what are snRNPs
small nuclear ribonucleoproteins
spliceosome with snRNA
where are 30s and 50s ribosome subunits assembled
in the nucleoid
64 codons but 20 aa means what
there is degeneracy
start codon
AUG
stop codons
UAA
UAG
UGA
open reading frame
stretch of DNA between the start and stop codon
aminoacyl tRNA
tRNA bound to amino acid
aa attatched to tRNA using aminoacyl-tRNA synthetase (enzyme) using energy from ATP
ribosome binding sites for tRNA
- A site: A for aminoacyl-tRNA, which first enters at this site.
- P site: P for peptidyl-tRNA, which carries the growing polypeptide. The polypeptide chain moves from the P site to the tRNA on the A site during peptide bond formation.
- E site: E for exit site. The tRNA from the P site is sent here and released from the ribosome.
what catalyzes the formatino of a peptide bond between the polypeptide in the P sie and the newly added aa in the A site
the ribosome
translocation
occurs in which the tRNA molecule at the A site moves to the P site, and the tRNA at the P site moves to the E site (A → P → E)
chaperonins
Specialized proteins known as chaperonins are found
in both eukaryotic and prokaryotic organisms and
function in assisting newly synthesized polypeptides
to fold into their correct shape.
translocation
A piece of one chromosome
breaks off and attaches to another chromosome. Translocation increases chromosomal arm length and results in an abnormal banding pattern. This is the only mutation that affects both chromosomes.
inversion
A portion of the chromosome becomes
inverted on the arm of the chromosome. Results in an abnormal banding pattern, but does not affect the length of the chromosome.
duplication
A piece of the chromosome is
duplicated, resulting in a larger chromosomal arm and an atypical banding pattern.
deletion
A portion of the chromosome is deleted,
resulting in a shorter chromosomal arm.
what are the types of chromosomal muations
occur and affect the entire
chromosome rather than individual nucleotides. There
are four types:
null mutation
non functional allele. is produced
lacks the functino of the normal wild-type allele
types of base substitutions
silent mutations
missense mutations
nonsense mutation
sielnt mutation
no change in amino acid sequence due to third base wobble due to degeneracy
missense mutations
single change in aa sequence
conservative- similar aa
non conservative- different aa
frameshirt
mutatinos that result in shift of reading frame
insertions
deletions
what are the factors that contribute to DNA mutations
DNA pol errors
loss of DNA durign meiosis crossing over
chemical damage from drugs
radation
transposons
what are transposons
jumping genes
DNA sequences in PROKARYOTES and EUKARYOTES that can move and
integrate into different places in the genome.
what factors prevent DNA mutations
DNA pol proofreading
mismatch repair - macheinery that checks uncaught erros
nucleotide excision repair- that cuts out damaged DNA and replaces it with correct DNA using complementary base pairing.
