Exam 2: Ch 4 -- Translation, DNA Replication, Repair, Recombination, and Viruses Flashcards
translation
process where nt sequence of mRNA is used as a template to join aas in a pp chain in the correct order
in cytoplasm
3 types of RNA used in translation
mRNA
tRNA
rRNA
mRNA
carries genetic information transcribed from DNA in a linear form
read in sets of 3 nt sequences called codons
each codon specifies an …
AA
tRNA
deciphers codons in mRNA
each aa has its own subset of tRNAs, which bind the aa and carry it to the growing end of the pp
contains anticodon that base-pairs with the complementary codon in mRNA
rRNA
associates with a set of proteins to form ribosomes
move along an mRNA to catalyze assembly of aas into proteins
large and small subunit
post-translational processing
pp chain undergoes additional folding, modifications, and association with other pps
how many codons
64
how many stop codons
3
UAA, UGA, UAG
most aas are encoded for by more than one …
codon
only Met and Trp have a single codon
which aas have 6 codons
leu, ser, arg
degenerate
a particular aa can be specified by multiple codons
start codon
AUG-Met
reading frame
sequence of codons from start to stop
aminoacyl-tRNA synthetase
catalyze chemical linkage between a tRNA and its aa forming an aminoacyl-tRNA
how many tRNAs in bacteria vs eukaryotes
30-40
vs
50-100
more tRNAs than…
aas
so many aas have more than 1 tRNA they can bind to
many tRNAs can pair with more than one codon
explains how there are more codons than tRNA
acceptor stem
3’ end of the unlooped aa with sequence CCA
wobble
unstandard pairing between bases
3rd base in mRNA codon and first base in tRNA anticodon
ex. antibodon with G in first (wobble) position on tRNA can pair with C or U in 3rd position on mRNA
example of wobble
phenylalanine codon UUU and UUC and recognized by tRNA GAA
inosine
deaminated product of adenine
found in tRNA wobble position and can recognize mRNA codons with A, C, or U in the 3rd wobble position
4/6 codons for Leu are recognized by tRNA with anticodon 3’-GAI-5’ b/c of inosine
cognate
compatible tRNAs
aminoacyl-tRNA synthetase rxn
aa linked to tRNA by a high-engergy bond and is said to be “activated”
energy of this bond drives formation of peptide bonds
how is aminoacylation driven toward activation
hydrolysis of phosphoanhydride bond in released PPi
how do aminoacyl-tRNA synthetases recognize their cognate tRNAs
interact with anticodon loop and acceptor stem
interact with other regions
proofreading of aminoacyl-tRNA synthetases
checks fit in aa binding pocket
if wrong aa, bound synthetase catalyzes removal of aa from tRNA
error rate in E. coli is 1/50,000 codons
the ______ is the most abundant RNA-protein complex in the cell
ribosome
rate of elongation by a ribosome
3-5 aa added per second
100-200 aa proteins made in a minute or less
ribosome structure
3 (bacteria) or 4 (eukaryotic) different rRNA molecules and up to 83 proteins
2 subunits
small subunit has 1 molecule of rRNA
large subunit has 1 molecule of large rRNA and 5.8s rRNA
Svedberg unit
rRNA and ribosomal subunits
measure of the sedimentation rate of macromolecules centrifuged under standard conditions (a measure of size)
tRNAiMet
binds at appropraite site on small ribosomal subunit (P site) to begin synthesis of a pp chain
eukaryotic translation initiation factors (eIFs)
mediate small and large ribosomal subunits assembling around an mRNA that has an activated initiator tRNAiMet positioned at start codon of P site
bind GTP and hydrolysis to GDP functions as proofreading
what is the start codon
first AUG (Met) downstream from the 5’ end in mRNA
Kozak sequence
5’-ACCAUGG-3’
elongation factor (EF)
proteins that mediate elongation in translation
translocation
movement of the ribosome one codon at a time along mRNA
steps of elongation
tRNAiMet attached to P site, new tRNA attaches to A site and GTP hydrolyzed to GDP
3’ end of tRNA in A site is close to 3’ end of tRNAiMet and a peptidyltransferase rxn is catalyzed by large rRNA subunit
ribosome translocates and empty tRNA moved to E site and tRNA with pp chain moved from A site to P site
release factor (RF)
2 types
eRF1
eRF3
eRF1
eukaryotic release factor 1
looks like a tRNA and binds A site when it reaches stop codon
eRF3
GTP binding protein that works with eRF1
cleaves peptidyl-tRNA to release the completed protein
ribosome recycling
post-termination complex is bound to ABCE1, which uses ATP hydrolysis energy to separate the ribosomal subunits and release mRNA
2 factors that increase rate a cell can synthesize a protein
simultaneous translation of a single mRNA by multiple ribosomes
rapid recycling of ribosomal subunits after they disengage from the 3’ end of an mRNA
polyribosome
translation of a single mRNA by multiple ribosomes
forms circle-like structure, where finished ribosomes start process again quickly
GTPase superfamily
switch proteins that cycle between GTP-bound active form and GDP-bound inactive form
hydrolysis of GTP causes a conformational change
used in initiation, elongation, and translocation
nonsense mutation
inactivates a gene by changing a base pair in a normal codon to the stop codon
forms nonfunctional proteins
nonsense mutations in E. coli
can be suppressed by a second nonsense mutation in a tRNA gene
changes anticodon to complement codon of mutated mRNA
conservative DNA replication
2 daughter strands form a new dsDNA and parental dsDNA remains intact
semiconservative DNA replication
parental strands permanently separated and each forms a dsDNA with the daughter strand base-paired to it
primer
short preexisting RNA or DNA strand beginning chain growth
DNA polymerase
uses a DNA primer to start chain growth
adds deoxynucleotides to free hydroxyl group at 3’ end of primer
5’ –> 3’ direction
helicase
enzyme that unwinds parental DNA beginning at replicatino origins
pimase
a special RNA polymerase that forms a short RNA primer to the unwound template strands
replication fork
DNA region where proteins come together to carry out replication
leading strand
replicated continuously from a single RNA primer in the 5’—> 3’ direction
lagging stand
a new primer is needed every few hundred bases and is elongated discontinuously in Okazaki fragments
PCNA
homotrimeric protein that has a central hole that daughter dsDNA passes through
known as a sliding clamp
daughter strands of DNA grow _________
bidirectionally
two replication forks assemble at the same origin and move in opposite directionss
ORC
6 subunit protein - orgin recognition comples
binds to each origin and associated with other proteins
primary mechanism for regulating DNA replication
controlling initiation
S-phase cyclin dependent kinase
regulates activation of MCM helicase, which initiates replication
mutation
change in normal DNA sequence
1st line of defense of preventing mutations
DNA polymerase itself
3’ –> 5’ exonuclease activity of some DNA polymerases
polymerase pauses, 3’ end of growing chain transferred to exonuclease site and incorrect base is removed
point mutation
change in a single base pair in DNA sequence
missense
point mutation that changes the codon for an aa
silent mutation
point mutation that does not change aa sequence
one of the most frequent point mutations
deamination of a cytosine base converts it into uracil
DNA excision repair system
segment of damaged DNA excised
gap filled by DNA polymerase and ligase using complementary DNA as a template
most common type of point mutation in humans
C to T caused by deamination of 5-methyl C to T
base excision repair
problem is recognizing which is the mutant DNA strand to make a repair
DNA glycosylase flips thymine out of helix then hydrolyzes the bond creating an AP (apruinic) site using endonuclease
DNA polymerase replaces missing base and ligase fills gap
occurs before DNA replicatino
depurination
loss of guanine or adenine from DNA resulting from hydrolysis of glycosylic bond
mismatch excision repair
eliminates base-pair mismatches and insertions or deletions of one or a few nts accidentally introduced by DNA polymerase
must determine which strand is the mutant strand
occurs after DNA replication
nt excision repair
fix DNA regions containing chemically modified bases (chemical adducts) that distort the normal shape of DNA locally
ex. thymine-thymine dimers are repaired
why is DNA damage in higher eukaryotes repaired much faster in regions of the genome being actively transcribed
shared subunits in transcription and DNA repair (transcription-coupled repair)
RNA polymerase is stalled at a lesion on DNA, protein CSB is recruited to RNA polymerase which opens the helix and TFIIH fixes it
2 things that cause ds breaks in DNA
ionizing radiation
anti-cancer drugs
ds breaks can lead to
gross chromosomal rearrangements
2 systems to repairs ds breaks
homologous recombination
non homologous end joining (NHEJ)
NHEJ
error-prone dominant mechanism for repairing ds breaks
rejoin nonhomologous ends of 2 DNA molecules
results in loss of several base pairs at joining point
could form mutagenic deletions
can NHEJ join broken ends of different chromosomes together?
yes, leads to translocations
BRCA genes participate in what repair system
homologous recombination
homologous recombination
damaged sequence is copied from an undamaged copy of the same chromosome of a diploid organism, or sister chromatid
DNA recombination in meiosis
regions of homologous chromosomes crossover to create genetic diversity
viruses
obligate intracellular parasites
use a host cell’s machinery to synthesize viral proteins and to replicate the viral genome
virion
infectious virus particle
consists of nucleic acid and an outer shell of protein that both protects the viral nucleic acid and functions in the process of host-cell infection
simplest viruses contain only enough RNA/DNA to code for ___ proteins, while the most complex can code ___ proteins
4, 200
surface of a virion
contains many copies of 1 type of protein that binds specifically to a receptor protein on a host cell
determines host range
host range
group of cell types a virus can infect
bacteriophage
virus that only infects bacteria
poliovirus affects cells in the
intestine
motor neurons in spinal cord causing paralysis
HIV-1 affects…
cells essential for the immune response called CD4+ T-lymphocytes - causes AIDS
neurons and glia
capsid
protein coat the encloses the nucleic acid of virion
composed of multiple copies of 1 protein of a few different proteins coded by a single viral gene
nucleocapsid
capsid + enclosed nucleic acid
how is the nucleocapsid arranged
helical structure in a groove inside a protein tube - rodlike
icosahedron solid - spherical object build of 20 faces of equilateral triangles (head)
envelope
external membrane covering the nucleocapsid
phospholipid bilayer and a few viral glycoproteins
plaque assay
number of infectious viral particles in a sample
culture dilute sample of viral particles on a plate covered with host cells
count number of local lesions (plaques)
when does a plaque develop
when a single virion infects a single cell
virus replicates and then lyses the cell to release progeny virions
virus clone
the progeny virions in a plaque
lytic cycle
adsorption
penetration
replication
assembly
release
lytic cycle: adsorption
virion binds multiple copies of capsid protein to specific receptors on cell surface
lytic cycle: penetration
viral genome crosses plasma membrane
viral proteins inside capsid can also enter in some cases
lyric cycle: replication
viral mRNAs are produced with the aid of host cell machinery (DNA virus) or viral enzymes (RNA virus)
mRNAs translated by host cell machinery
lytic cycle: assembly
viral proteins and replicated genomes associate to form progeny virions
lytic cycle: release
infected cell is lysed or disintegrates gradually
rabies
virion adsorbed by endocytosis and release of progeny virions occurs by budding from plasma membrane
temperate phages
establish nonlytic association with a host cell that does not kill
lysogeny
integrated viral DNA (prophage) is replicated as part of the cell’s DNA from one generation to the next
part of temperate phages
retroviruses
enveloped viruses with a genome consisting of 2 identical strands of RNA
RNA genome is a template for forming DNA by reverse transcriptase
