DAT Molecular Genetics Flashcards
DNA
A, T, C, G; the hereditary
information of the cell; contains a double
helix with major and minor grooves
DNA backbone
consists of 5’ to 3’
phosphodiester bonds to form a sugar-
phosphate backbone
RNA
A, U, C, G; has functional usage in
the cell; varies per type (mRNA is linear,
tRNA is in a clover shape, while rRNA is
globular)
DNA replication
begins at origins of
replication in the middle of a DNA
molecule
DNA strands separate to form
replication
bubbles that expand in both directions.
How many origin of replication do prokaryotes have
1
first step of DNA replicaiton
A second chromatid containing a copy
of DNA is assembled during interphase
Second step of DNA replication
Helicase is the enzyme that unwinds
DNA, forming a Y shaped replication
fork -
Single stranded binding proteins
attach to each strand of
uncoiled DNA to keep them separate
Topoisomerases
break and rejoin the DNA double
helix of the replication fork,
preventing knots
Third step of DNA relication
DNA polymerase moves from the 3’ →
5’ direction only, and synthesizes a new
strand that is antiparallel (5’ → 3’) -
Okazaki fragments
DNA ligase connects these, strand, the DNA
polymerase has to go back to the
replication fork and work away from
it. It produces fragments piece by
piece, and these fragments are called
Okazaki fragments
Fourth Step of DNA replication
Primase is an enzyme that creates a
small strip of RNA off of which DNA
polymerase can work since it can only
add to an existing strand
DNA replication requires
RNA primer
Every Okazaki fragment has
an RNA primer
what are RNA primers replaced with?
DNA by DNA polymerase i
DNA polymerase 3 main function
mainly for
replication
Polymerases I and III have..
3’ → 5’
exonuclease function, meaning
that they can break the
phosphodiester backbone on a
single strand of DNA and remove
a nucleotide. An exonuclease can
only remove from the end of the
chain.
Polymerase III also has some…
proofreading function
Polymerase I also has
5’ → 3’
exonuclease function to remove the
primer; polymerase I can also
proofread in the 3’ → 5’ direction
when laying down a new nucleotide
strand
helicase
unzips DNA to form
replication fork
Ligase -
‘glues’ two strands of DNA
together
Once the DNA has been replicated, we still need
to replicate..
the telomeres
what are telomeres termed as?
the aglets of a chromosome since they
protect the DNA from degradation by enzymes.
Telomerase carries an
RNA template and
binds to the flanking 3’ end of the telomere
that compliments part of its RNA,
mRNA
- a single stranded template;
HOW many triplet codons are there
64
what is the least abundant RNA molecule
mRNA (high turnover rate)
what are the three stop codons
UAA,
UAG, and UGA
tRNA
a clover shaped transporter of
anticodons;
Wobbles
the exact base pair of the
third nucleotide in the codon is often
not required, allowing 45 different
tRNA’s to base-pair with 61 codons
that code for amino acids
what is tRNA’s clover shape held together by
hydrogen bonds
what Is the tiniest RNA molecule
tRNA
rRNA
come together to form
ribosomes.
nucleolus
an assemblage
of DNA actively being transcribed into
rRNA,
A ribosome has how many binding sites
4 total, 1 for mRNA and 3 for tRNA
Transcription
serves to create RNA molecules
from a DNA template in the nucleus.
First step of transcription
Initiation - RNA polymerase attaches to
the promoter region on DNA and unzips
the DNA into two strands.
TATA box.
A promoter
region for mRNA transcription often
contains a repeating sequence of A and T
nucleotides
consensus sequence
most common sequence of
nucleotides at the promoter region
what is the TATA box called in prokaryotes
‘Pribnow
box’
step 2 of transcription
Elongation - RNA polymerase continues
unzipping DNA and assembles RNA nucleotides using one strand of DNA as
a template.
Termination
occurs when RNA
polymerase reaches a special sequence,
often AAAAAA in eukaryotes
what direction does transcription occur
3’ to 5’
mRNA Processing modifications
5’ cap (5’ G-P-P-P-):, A poly-A tail (-A-A-A…A-A-3’):, RNA splicing, Alternative splicing
5’ cap (5’ G-P-P-P-):
this sequence is
added to the 5’ end of the mRNA; a
guanine with 3 phosphate groups (GTP)
provides stability for mRNA and a point
of attachment for ribosomes
A poly-A tail (-A-A-A…A-A-3’):
this
sequence is attached to the 3’ end of
the mRNA, The poly A tail consists of 200 A
nucleotides that serve to provide stability
and control the movement of mRNA
across the nuclear envelope
RNA splicing
removes nucleotide
segments from mRNA before mRNA
moves into the cytoplasm via small
nuclear ribonucleoproteins (snRNP’s). The
spliceosome deletes the introns and
splices the exons. Prokaryotes have no
introns
Alternative splicing
allows different mRNA to be generated from
the same RNA transcript by selectively
removing differences of an RNA
transcript into different combinations
Translation
assembly of polypeptides based on reading
of new RNA in the cytoplasm with GTP used as
the energy source.
First step of translation
Initiation - the small ribosome subunit
attaches to the 5’ end of mRNA; a tRNA
methionine attaches to the start
sequence of mRNA (AUG), and the
large ribosomal subunit attaches to
form a complete complex. Requires 1
GTP.
second step of translation
Elongation - next tRNA binds to the A
site, peptide bond formation occurs,
and the tRNA without methionine is
released. The tRNA currently in the A
site moves to the P site (translocation)
and the next tRNA comes into the A site
to repeat the process. This requires 2
GTP per link.
third step of translation
Termination - when the ribosome
encounters the stop codon (either UAG,
UAA, or UGA), the polypeptide and the
two ribosomal subunits all release due
to a release factor breaking down the
bond between tRNA and the final amino
acid of the polypeptide
fourth step of translation
Post-translation - translation begins on
a free floating ribosome; a signal
peptide at the beginning of the
translated polypeptide may direct
what is the amino acid for start codons in eukaryotes
methionine
Silent mutations
when a mutation
occurs, but the new codon still codes for
the same amino acid, therefore the
effect is “silenced”
Nonsense mutations
the
new codon codes for a stop codon
Neutral mutations
there is
no change in protein function
Missense mutations
a new codon
codes for a new amino acid → can have
minor or fatal results (as in sickle cell
anemia where glu → val)
Proofreading
DNA polymerase checks
base pairs
Mismatch repair
enzymes repair the
errors DNA polymerase missed —
mismatch repair deals with correcting
mismatches between normal bases
Excision repair
enzymes remove
nucleotides damaged by mutagens
Nucleotide excision repair
can be
used to repair issues like thymine
dimers
Base excision repair
similar in
function to nucleotide excision repair,
but uses different enzymes. The main
difference is that nucleotide excision
repair will chunk out an entire
segment around the faulty base by
nicking the entire surrounding
phosphodiester backbone, not just
the faulty base.
The key structure
responsible for DNA organization
nucleosome
Nucleosome
structure formed when
DNA is coiled around bundles of 8-9
histone proteins, kind of like beads on a
string
Euchromatin
chromatin is
loosely bound to nucleosomes;
present when DNA is actively
being transcribed
Heterochromatin
areas of
tightly packed nucleosomes
where DNA is inactive and
appears darker.
Transposons (jumping genes)
DNA segments that can move to a new
location on either the same or different
chromosome.
Pseudogenes
former genes that
have accumulated mutations over a
long time and no longer produce a
functional protein
Virus - consist of the following:
Nucleic acid, Capsid, Capsomeres, Viral envelope
Nucleic acid
RNA or DNA that can
be double or single stranded
Capsid
a protein coat that encloses
the nucleic acid
Capsomeres
assemble to form the
capsid
Viral envelope
surrounds capsid of
some viruses and incorporates
phospholipids and proteins obtained
from the cell membrane of the host
Bacteriophage
a virus that only attacks
bacteria, is usually specific to a type of
cell via viral surface proteins binding to
specific receptors on the host cell of the
species.
Host range
term used to
define the range of organisms or species a virus
can attack
Viral replication
2 cycles: the lytic cycle, DNA viruses
Lytic cycle
when the virus penetrates
the host cell membrane and uses host
machinery to produce nucleic acids
and viral proteins that are then
assembled to make new viruses
DNA viruses
replicate by first
replicating DNA and forming new
viral DNA, which is then
transcribed to produce viral
proteins that combine with DNA
to form new viruses
RNA virus
RNA serves as mRNA
which is translated into protein.
This protein and RNA assemble to
form a new RNA virus
Retroviruses
single stranded
RNA viruses that use reverse
transcriptase to make a DNA
complement of their RNA by
hijacking the host cell’s replicating
machinery. This DNA is then used
to manufacture mRNA or enter
the lysogenic cycle (becoming
incorporated into the host DNA)
Lysogenic cycle
when viral DNA is
incorporated into the DNA of the
host cell;
2 phases of lysogenic cycle
a. Dormant stage - the virus is
referred to as a provirus
(prophage if a bacteriophage) and
remains inactive until an external
stimuli triggers the virus
b. When triggered, the virus enters
the lytic cycle, and follows the
same steps as mentioned in the
previous bullet
Prions
are not viruses or cells, but are
infectious, mis-folded versions of proteins
in the brain that cause normal versions of
proteins to also become mis-folded.
Prions are fatal, and are implicated in
diseases such as Mad Cow disease, kuru,
scrapie in sheep, and Creutzfeldt-Jakob
disease
Viroids
very small (even smaller than
viruses!) circular RNA molecules that
infect plants. These do not encode for
proteins, but replicate in host plant cells
via host enzymes, and cause errors in the
regulatory systems of plant growth
Binary fission
bacteria reproduce via
this method in which the chromosome
replicates, the cell divides into two cells,
and each cell now holds the exact same
copy of the original chromosome
Plasmids
short, circular DNA outside
of chromosomes that carry genes that
are beneficial, but not essential for
survival
Episomes
plasmids that can
incorporate into bacterial
chromosomes
Genetic exchanges
there are three
main ways bacteria can exchange
information with each other or their
surroundings : Conjugation, Transduction, Transformation
Conjugation
donor bacteria
produces a bridge (pilus) and
connects to the recipient bacteria;
this allows the donor to send a
chromosome or plasmid to the
recipient, thus allowing
recombination to occur
Transduction
DNA is introduced
into a genome via virus. When the
virus is assembled during the lytic
cycle, some bacterial DNA is
incorporated in the place of viral
DNA. When the virus infects another
host, the bacterial DNA part that it
delivers can recombine with the
resident DNA.
Transformation
bacteria take in
DNA from surroundings and
incorporate it into the genome
Operon
region of DNA that controls
gene transcription and consists of: Promoter, Operator, Structural genes, Regulatory genes
Promoter
sequence of DNA where
RNA polymerase attaches to begin
transcription
Operator
region that can block
action of RNA polymerase if occupied
by repressor proteins
Structural genes
DNA sequences
that code for related proteins
Regulatory genes
located outside
of operon region, and produce
repressor proteins. Others produce
activator proteins that assist the
attachment of RNA polymerase to the
promoter region
Lac operon (E. coli)
controls the
breakdown of lactose; the regulatory
gene produces an active repressor that
binds to the operator and blocks RNA
polymerase
Trp operon (E. coli)
produces enzymes
for tryptophan synthesis; regulatory
genes produce an inactive repressor,
which allows RNA polymerase to produce
enzymes.
Repressible enzymes
are
when structural genes stop producing
enzymes only in the presence of an active
repressor.
Regulatory proteins
repressors and
enhancers/activators that influence RNA
polymerase attachment to the promoter
region.
Nucleosome packing
Methylation of histones, Acetylation of histones, Direct DNA methylation
Methylation of histones
results in
tighter packing that prevents
transcription
Acetylation of histones
uncoils
chromatin, encouraging transcription
Direct DNA methylation
epigenetic control of DNA that can
be inherited and usually leads to
lower expression
RNA interference
noncoding RNA
(ncRNA) plays a role in controlling gene
expression as well! Some are even
involved in chromatin modification.
Micro RNA (miRNA)
single stranded
RNA molecules that bind to
complementary RNA sequences and
either degrade the target or block its
translation
Short interfering RNA (siRNA)
function similarly to miRNA,
