Exam 3 Flashcards
DNA replication model
semiconservatively
prokaryote DNA replication
one piece of circular DNA
helicase
unwinds the helix at the replication fork
singel strand binding protein (SSBP)
binds to a stabilizes the single-stranded templates
topoisomerase
causes single-strand breaks that allows the DNA to unwind
relieves supercoil strain by causing breaks in DNA
initiation
unwinding the DNA, starting at the origin
initiator proteins bind to the origin
initiator proteins
helicase
SSBP
Topoisomerase
elongation
DNA polymerase adds nucleotides to the separate strands
nucleotides come from somewhere in the nucleus
primer
RNA polymerase
gives it the free 3’ end to start
okazaki fragments
form from discontinuous synthesis of the lagging strand
each fragment needs separate RNA primer
termination
all the proteins fall off and replication forks meet
many things can damage DNA
chemical assaults
x-rays
UV light
radioactive emissions
spontaneous chemical changes to nucleotides
Central Dogma
from DNA, to RNA, to protein
or RNA directly to protein
transcription
synthesis of RNA under the direction of a DNA template
initiation, elongation, termination
transcription prokaryotes
in cytosol
DNA –> mRNA
duplicates one strand to make mRNA and then re-zips the original strands
RNA polymerase
binds to the template strand, unzips the strand, and copies the coding strand which becomes the mRNA
promoter
where RNA polymerase binds, the starting location
transcription initiation complex
formed when RNA polymerase and associated transcription factors bind to the promotor
transcription termination in prokaryotes
polymerase hits terminator sequence and falls off template
transcription termination in eukaryotes
transcription continues for 10-35 more nucleotides and then transcript is cleaved from the template while polymerase continues for several 100 nucleotides
point mutations
insertion, deletion, substitution
silent mutation
does not affect protein sequence
missense mutation
codes for new type of amino acid
nonsense mutation
stop codon comes early
frameshift
insert new that changes all amino acids beyond that point
prokaryotic processing (transcription)
RNA codes for proteins ready to use right away
eukaryotic processing (transcription)
RNA must be processed in the nucleus into Pre-RNA, modifying the 5’ end and 3’ end
protects from degradation, transports to cytoplasm, recognition by ribosomes, removal of introns and splicing of exons
RNA splicing
intron punched off and exons connected together
results in mature mRNA
domain
modular architecture of proteins
importance of introns
regulate gene expression
translation
converts the coded information into a sequence of amino acids (protein)
codon
a triplet of nucleotides
degenerate code
each amino acid is represented by multiple codons (the 44 are used)
crick’s adaptor hypothesis
20 adaptors (one for each amino acid)
adaptor = bifunctional RNA (binds to an amino acid and has another site to bind to codon)
where does translation get energy
GTP
Translation initiaion
sets reading frame
translation elongation and translocation
repeat elongation and translocation
protein built in N-term to C-term direction
Termination of translation
stop codon, releases
posttranslational modifications
folding
covalent attachments
S-S bridge
proteolytic cleavage
multi-subunit association (quaternary structure)
protein targeting
proteins have amino acid signals that direct the proteins to the right place
protein targeting compartments
cytosol
nucleus
mitochondria
chloroplasts
peroxisomes
endoplasmic reticulum
nuclear envelope
golgi
lysosomes
start in cytosol then move to RER
protein targeting I
proteins completely synthesized in the cytosol are synthesized by free ribosomes
Protein Targeting II
proteins destined for the endomembrane system or for secretion begin on free ribosomes then move to RER membrane
constitutive gene expression
some genes are always expressed
gene expression levels
translational…fast but energy costly
post translational…fast but energy costly
trancriptional..slower but energy efficient
operon
gene cluster composed of the promoter, operator, and transcription unit that codes for an mRNA
operator
overlaps promoter or between promoter and transcription
on/off switch
transcription unit
genes that are read and transcribed
negative regulation (translation)
genes normally on, and binding repressor turns transcription off
positive regulation (translation)
requires binding of an activator protein to start transcription
trp operon
repressible operon turned off by repressor proteins
repressor (trp)
allosteric protein…needs a corepressor to function, so the operon is not turned off all the time even though the repressor is always present
allosteric protein
active = functional
inactive = nonfunctional
binding a regulator stabilizes into:
activator = active conformation
inhibitor = inactive conformation
tryptophan
allosteric effector/corepressor to activate trp repressor
inducible operon
normally off because of active repressor and turned on in the presence of an inducer, which inactivates the repressor
lac operator
prevents RNA polymerase from binding to promoter, but it binds to the operon without a corepressor
trp
repressible
repressor normally unbound adn then binds to stop actiivty
anabolic pathways
lac
inducer
normally bound stopping actively, and then unbinds to allow activity
catabolic pathways
E. coil and glucose
uses glucose when available (senses with cAMP)
activates genes for lactose metabolism when lactose is present
In what kind of molecule is the genetic code stored for SARS-CoV-2? How do mRNA vaccines help protect from future infections? Where does protein synthesis start and end for the
spike proteins of SARS-CoV-2?
RNA sequence
mRNA teaches your body to code for the proteins that fight the virus
starts in cytosol ends in RER
primase
synthesizes an RNA primer
transcription factors
proteins that help regulate transcription,
bind to DNA or other proteins to help RNA polymerase bind to the promoter
posttranscriptional modification/RNA processing
splicing, capping, and addition of a poly A tail
e site
exit
a site
activate
p site
polypeptide bond
TATA box
binding site for transcription factor in promoter
RNA Processing example
Retinitis Pigmentosa results from the wrong assortment of exons
DNA accessibility example
Calico cats color is due to random inactivation of x chromosomes
