DAT bio chapter 6 Flashcards
Nucleotide
ribose sugar, nitrogenous base, and
phosphate group.
Nucleoside
- ribose sugar and nitrogenous base.
DNA is a polymer of what
nucleotides
DNA has what on the 2 carbon on the ribose sugar
hydrogen
RNA has what on the 2 carbon on the ribose sugar
OH (hydroxyl group
In DNA. Adenine binds to what with how many bonds
Thymine
2 hydrogen bonds
In DNA. Guanine binds to what with how many bonds
cytosine
3 hydrogen bonds
In RNA, adenine binds to what
uracil
2 hydrogen bodns
T/F greater temp is needed to break the G-C bonds
true, due to more bonds
What are nucleosomes
are complexes of DNA wrapped
around histone proteins.
How many histones do each nucleosomes contain?
9
The central core of the nucleosome contains how many of each histone?
contains two
of each histone H2A, H2B, H3 and H4.
T/F On the
outside of the nucleosome, a single histone, H1, holds the DNA in
place.
true
Chromatin
Functions in condensing the the structure of dna and his tones into a more compact structure
Two types of chromatin
- Euchromatin
2. Heterochromatin
Euchromatin
nucleosomes are “loosely
packed”, so DNA is readily accessible for
transcription.
Heterochromatin
nucleosomes are “tightly
packed”, so DNA is mostly inactive.
what charges are histones and DNA
Histones are positively charged while DNA is
negatively charged, allowing proper binding.
Acetylation of histones does what
removes positive charges,
relaxing DNA-histone attractions and allowing for
more transcription to happen.
Deacetylation of histones does what
increases positive
charges, tightening DNA-histone attractions and
decreasing transcription.
Methylation of histones does what
adds methyl groups,
either increasing or decreasing transcription.
What is the origin of replication?
required to initiate DNA
replication where the DNA strands first separate.
Multiple vs single origin of replication
Organisms with circular DNA such as bacteria
have a single origin of replication while organisms
with linear DNA such as humans have multiple
origins of replication.
What does it mean for DNA to undergo semiconservative replication?
it means the each new double helix produced by
replication has one “new” strand and one “old”
strand.
What does it mean for DNA to be antiparallel
5’ end
(terminal phosphate group) of one strand is
always next to the 3’ end (terminal hydroxyl
group) of the other strand and vice versa.
Steps of DNA replication
- initiation
- elongation
- termination
Step 1 of DNA replication
- initiation
- creating origins of replication at
A-T rich segments of DNA because A-T bonds
only have two hydrogen bonds and are easier
to split apart.
Step 2 of DNA replication
- Elongation
producing new DNA strands using
different types of enzymes.
Elongation 1 (helicase)
Helicase unzips DNA by breaking hydrogen
bonds between strands, creating a
replication fork.
Elongation 2 (Single-strand binding proteins)
bind to
uncoiled DNA strands, preventing
reattachment of the strands to each other.
Elongation 3
Topoisomerase
nicks the DNA double
helix ahead of helicase to relieve built-up
tension.
Elongation 4
Primase
places RNA primers at the origin
of replication to create 3’ ends for
nucleotide addition.
Elongation 5
Sliding clamp proteins
hold DNA
polymerase onto the template strand.
Elongation 6
DNA polymerase
Enzyme that extends dna in the 5 to 3 direction
Elongation 7
The leading strand
produced
continuously because it has a 3’ end that
faces the replication fork.
Elongation 8
● The lagging strand
is produced
discontinuously because its 3’ end is facing
away from the replication fork. Thus, many
RNA primers are needed to produce short
DNA fragments called Okazaki fragments.
Elongation 9
A different DNA polymerase
replaces RNA
primers with DNA.
Elongation 10
DNA ligase
glues separated fragments of
DNA together.
Termination
replication fork cannot
continue, ending DNA replication.
Termination part 1
Telomeres
are noncoding, repeated
nucleotide sequences at the ends of linear
chromosomes. They are necessary in
eukaryotes because 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).
Termination part 2
Telomerase
enzyme that extends
telomeres to prevent DNA loss.
DNA replication happens in which part of the cell cycle
S phase
Summary of transcription
Genes are instructions within DNA that code for
proteins. However, they must first be transcribed
into RNA before being translated into proteins.
Specifically, DNA undergoes transcription to
produce single-stranded messenger RNA (mRNA).
Steps for transcription
Initiation
Elongation
Termination -
Initiation for transcription
a promoter sequence (aka
promoter) next to the gene attracts RNA
polymerase to transcribe the gene.
Initiation for elongation
- transcription bubble forms and
RNA polymerase travels in the 3’ → 5’ direction
on the template strand. However, it extends
RNA in the 5’ → 3’ direction.
Initiation for Termination -
a termination sequence (aka
terminator) signals to RNA polymerase to
stop transcribing the gene.
Where does transcription happen in the prokaryotes
cytosol
First step of transcription in prokaryotes
RNA polymerase opens up DNA, forming a
transcription bubble.
second step of transcription in prokaryotes
Before transcription can occur, a sigma factor
combines with prokaryotic core RNA
polymerase to form RNA polymerase
holoenzyme, giving it the ability to target specific
DNA promoter regions.
What is an operon?
group of genes that function as a
single unit that is controlled by one promoter.
what is the operator region?
present near the operon’s
promoter and binds activator/repressor
proteins to regulate the promoter.
what is lac operon
inducible operon (it must be induced to become active).
What three genes are contained within the lac operon and what do they do
LacZ, lacY, and lacA
encode proteins required for lactose
metabolism.
When is lac operon used>
when glucose is not available as an energy source,
so lactose must be used.
First way lac operon can be controlled
BY Lac repressor protein
What gene encodes for lac repressor protein
LACL, which is always on
How does lac repressor protein block transcription?
by constantly binding to the operator
What happens to lac repressor protein when lactose is present?
converted to allolactose.
What does allolactose do?
binds directly to the repressor and
removes it from the operator, allowing
transcription to occur.
Second level of lac operon regulation
cAMP levels and catabolite activator protein
CAP
cAMP levels are ______ related to glucose levels,
Inversely,
when glucose is low, cAMP is high.
What does cAMP bind to?
to catabolite activator protein (CAP), which then
attaches near the lac operon promoter to help
attract RNA polymerase, promoting transcription.
Another operon employed by prokaryotes
trp operon,
trp operon responsible for what
producing the
amino acid tryptophan.
Try operon is known as….
repressible operon because it codes for
tryptophan synthetase and is always active
unless the presence of tryptophan in the
environment represses the operon.
Tryptophan binds to
trp repressor protein, which then attaches to the operator on the trp
operon to prevent tryptophan production.
What happens when tryptophan is not present in the environment>
trp operon will undergo transcription because the
trp repressor protein will be inactive.
eukaryotic transcription
occurs where
occurs in the nucleus and uses RNA polymerase
II to transcribe most genes.
what is needed in eukaryotes to help RNA polymerase bind to promoters?
Transcription factors
what is the tata box>
sequence in many promoters that
transcription factors can recognize and bind to.
Enhancers
DNA sites that activator
proteins can bind to; they help increase
transcription of a gene.
Silencers
DNA sites that repressor
proteins can bind to; they decrease
transcription of a gene.
Where are enhancers and silencers located?
far upstream or downstream form the gene. They loop around to colocalize
with RNA polymerase.
The poly A signal is located where
within the terminator
sequence and stimulates polyadenylation
(addition of adenine nucleotides to the 3’ end of
the mRNA).`
Post-transcriptional modification
conversion of pre-mRNA into processed mRNA,
which leaves the nucleus.
three
main types of post-transcriptional modification:
5’ capping
Polyadenylation of the 3’ end
Splicing out introns
5’ capping
- 7-methylguanosine cap is added
to the 5’ end of the mRNA during elongation,
protecting the mRNA from degradation.
Polyadenylation of the 3’ end
- addition of
the poly A tail to the 3’ end to prevent
degradation.
Splicing out introns
- introns are stretches of
noncoding DNA that lie between regions of
coding DNA (exons). Splicing refers to
removing introns from pre-mRNA using
spliceosomes. “Splice signals” present within
introns signal to the spliceosome where to cut.
(Eukaryotic Post-Transcriptional Modifications)
snRNAs (small nuclear RNA) and proteins make what
the functional part of a spliceosome and are
collectively referred to snRNPs (small nuclear
RiboNucleic Proteins).
(Eukaryotic Post-Transcriptional Modifications)
Alternative splicing
a single pre-mRNA
having multiple possible spliced mRNA products.
Thus, the same pre-mRNA can produce many
different proteins.
Important players in translation
Ribosomes and tRNA (transfer RNA) are
what is translation
process of
converting mRNA into protein products.
Ribosomes
made up of one small subunit and
one large subunit as described below:
eukaryotes ribosomes
small (40S) and large (60S) subunits form a 80S ribosome. They are composed of rRNA (ribosomal RNA) and proteins. The subunits are made in the nucleolus and assembled once they are exported to the cytosol.
prokaryotes ribosomes
small (30S) and large (50S)
subunits form a 70S ribosome. They are also
composed of rRNA and proteins, but are
assembled together in the nucleoid.
what is a codon
a group of three mRNA bases (A, U, G,
or C) that code for an amino acid or terminate
translation.
how many combinations of codon is there
64 codon combinations
total but only 20 amino acids, so degeneracy is
present (multiple codons code for the same amino
acid).
Start codon:
AUG
STOP CODON
UAA, UAG, UGA
what is an anticodon
group of three tRNA bases (A,
U, G, or C) that base pairs with a codon. Each tRNA
carries an amino acid to be added to the growing
protein.
Aminoacyl-tRNA
tRNA bound to an
amino acid.
Aminoacyl-tRNA synthetase
enzyme that
attaches an amino acid to a specific tRNA using the
energy from ATP.
Ribosomal binding sites for tRNA:
A site - A for aminoacyl-tRNA, which first
enters at this site.
2. P site - P for peptidyl-tRNA, which carries the
growing polypeptide.
3. E site - E for exit site. The tRNA from the P site
is sent here and released from the ribosome.
The ribosome catalyzes the formation of what
a peptide
bond between the polypeptide in the P site and
the newly added amino acid in the A site.
What happens after the formation of a peptide bond between the polypeptide in the p site and the newly added amino acid in the a site
the polypeptide is transferred to the A
site’s tRNA and the ribosome shifts one codon
down the mRNA. The A site will now be empty and
ready to accept another aminoacyl-tRNA. The tRNA
from the P site will be transferred to the E site and
will leave the ribosome.
What is DNA mutation
a heritable change in the
DNA nucleotide sequence that can be passed
down to daughter cells.
Three main types of DNA mutations:
Base substitutions (point mutations)
Insertions
Deletions -
Base substitutions (point mutations)
one nucleotide is replaced by another.
Silent mutations
part of base substitutions
no change in amino acid sequence. Due to “third base wobble”, mutations in the DNA sequence that affect the third base of a codon can still result in the same amino acid being added to the protein. Relies on the degeneracy (redundancy) of translation.
Missense mutations
part of base substitutions
single change in amino acid sequence. Can either be conservative (mutated amino acid similar to unmutated) or non-conservative (mutated amino acid different from unmutated).
Nonsense mutation
part of base substitutions
- single change in
amino acid sequence that results in a stop
codon. Results in early termination of
protein.
Insertions
- adding nucleotides into the DNA
sequence - can shift the reading frame.
Deletions
removing nucleotides from the
DNA sequence - can shift the reading frame.
Factors that contribute to DNA mutations:
DNA polymerase errors during DNA replication. Loss of DNA during meiosis crossing over. Chemical damage from drugs. Radiation.
Factors that prevent DNA mutations:
● DNA polymerase proofreading by DNA polymerase. ● Mismatch repair machinery that checks uncaught errors. ● Nucleotide excision repair that cuts out damaged DNA and replaces it with correct DNA using complementary base pairing.
Are viruses living or non living
non living, they must infect living cells to multiply
capsid (virus)
viral protein coat that is made of
subunits called capsomeres.
phospholipid envelope
some viruses pick this up
from the host cell membrane.
Two viral life cycle types:
lysogenic
lytic
Lysogenic cycle
virus is considered dormant
because it inserts its own genome into the
host’s genome and does not harm the host.
Each time the host genome undergoes
replication, so does the viral genome.
Lytic cycle
virus takes over host to replicate
and does cause harm to the host. The viral
particles produced can lyse the host cell to
find other hosts to infect.
Bacteria are what and how do they divide
asexual
binary fission
so they only receive genes from one parent cell
and do not increase genetic diversity through
reproduction.
How do bacteria must increase genetic diversity
through horizontal gene transfer
What is horizontal gene transfer
the transfer of genes between individual
organisms.
three methods of
horizontal gene transfer:
Conjugation
transformation
transduction
Conjugation
bacteria use a cytoplasmic
bridge called a pili to copy and transfer a
special plasmid known as the F plasmid
(fertility factor). If a bacteria contains an F
plasmid, it is referred to as F+. If not, it is
referred to as F-. To review, plasmids are
circular DNA pieces that are independent from
a bacteria’s single circular chromosome.
transformation
bacteria take up extracellular
DNA. Bacteria are referred to as competent if
they can perform transformation.
Electroporation is the process of using
electrical impulses to force bacteria to become
competent.
Transduction
viruses transfer bacterial DNA
between different bacterial hosts. This occurs
when a bacteriophage enters the lysogenic
cycle in its host and carries bacterial DNA
along with its own genome upon re-entering
the lytic cycle.
