Exam 3 material Flashcards
Freidrich Miescher identified
Nuclein
What was nuclein later renamed?
Nucleic Acid
What did Kossel and Levene show that DNA consisted of?
sugar, nitrogenous bases, and phosphate
what was the conundrum of the time of discovering DNA?
Proteins are more complex than DNA (20 amino acids vs. 4 nitrogenous bases), therefore it was thought that proteins Must be the genetic material
What was the first key experiment that lead to the identification of DNA as a genetic material?
Frederick Griffith’s Streptococcus pneumococcus experiment
Describe the Streptococcus pneumococcus experiment
bacteria from the S strain were killed by heat, and their remains were added to R strain bacteria. While neither alone harmed the mice, the combination was able to kill its host. Griffith was also able to isolate both live R and live S strains of pneumococcus from the blood of these dead mice.
what was the process called that happened in the Streptococcus pneumococcus experiment
transformation
what is key idea #1 that Avery, MacLeod and
McCarty demonstrated that
DNA is the transforming
principle
A mixture of things
has an effect on something.
Separate the components,
see which one has the effect.
what is key idea #2 that Avery, MacLeod and
McCarty demonstrated that
DNA is the transforming
principle
A mixture of
things has an effect on
something. Delete
components one by one, see
which deletion cause the
effect to disappear.
Hershey-Chase experiment
Label phage DNA with 32P and phage proteins with 35S, then infect bacteria, let the
‘injection’ occur, then tear off the virus and see what got injected into the bacteria
Structure of DNA
Nucleotide = base + pentose + phosphate
Chargaff’s Rule
Most importantly, A=T and G=C, that is A and T were
present in equimolar amounts as were G and C, and A+T does not equal G+C
Three rules to the structure of DNA
5’ to 3’; anti-parallel; complementary base pairing
What do the 5’ end have that the 3’ end doesn’t?
phosphate
What does the 3’ end have that the 5’ end doesn’t?
OH group
How many Hydrogen bonds does A-
T have?
two
How many hydrogen bonds does G-C have?
three
Which are more stable, A-T or G-C base pairs?
G-C
Properties of the DNA Double Helix
-Two DNA strands
wrapped in a right-
handed helix
-The bases are stacked
one on top of the other
(hydrophobic
interactions and van der
Waals forces stabilize
the helix)
-10 bases per helical turn
-Spaces between the turns of the
helix forms major and minor
grooves - important sites for
DNA/protein interactions
Central dogma
DNA -> RNA -> Protein
Chromosomes
very long, single DNA
molecules associated with proteins that
fold and pack the DNA into a compact
structure
(10,000-fold compaction)
Chromatin
the complex of DNA and
associated proteins is called
Gene
a segment of DNA that
contains the instructions for making a
particular protein or RNA
Genome
the total DNA complement
of an organism
Karyotype
an ordered display of
chromosomes in the nucleus of a
eukaryotic cell
what do chromosomes contain?
telomeres, replication origins and
centromeres – specialized sites needed for correct replication and segregation of genetic information
_______ chromosomes are organized within the nucleus
interphase
What enables
DNA packaging?
histones
Nucleosomes are the basic units of
___________ chromatin structure
eukaryotic
Five histones
-H2A, H2B, H3 and H4 (nucleosome core)
– H1(required for 30 nm fiber packing level)
Bacteria don’t have __________
nucleosomes
ATP dependent chromatin remodeling complexes…
utilize the energy from ATP hydrolysis to reorganize chromatin and, hence, regulate gene expression.
Acetylation (lysine)
removes positive charge, reducing affinity of histone to DNA – makes DNA more accessible for replication
Methylation
can either increase or decrease DNA accessibility, depending on the amino acid it is added to
Heterochromatin
condensed; – about 10% of interphase chromosome
most heterochromatin does not contain genes
Euchromatin
more loose structure (different from heterochromatin)
_______ chromosomes contain different forms of chromatin
interphase
Heterochromatin can be used to silence _______
unwanted gene expression
What causes Calico cat coloration?
patterns of X chromosome inactivation
DNA replication is
Semiconservative
Who did the experiment that proved that DNA is not replicated as a conservative method?
Meselson and Stahl
Are replication origins more likely to be A-T rich or G-C rich?
A-T because there are less Hydrogen bonds there
Initiator proteins…
allow the separation of the dsDNA
Replication machine
group of proteins that are recruited to the site and
replicate the DNA after separation of double helix
What is DNA synthesis is catalyzed by?
DNA polymerase
Nucleotides are added only to the which end of a DNA strand?
3’
DNA synthesis is 5’ to 3’
5’ to 3’
Proofreading
DNA Polymerase also has
an error-correcting activity
If DNA is synthesized only in the 5’ to 3’ direction
how are both strands replicated?
Leading and lagging strands
Is the replication fork symmetrical or asymmetrical?
asymmetrical
Primase
synthesize RNA
primer to begin replication
DNA polymerase extends what until it runs into the next RNA primer?
Okazaki fragment
RNA primer will then be
degraded by
ribonuclease
DNA polymerase called ___________________________ replaces the RNA with DNA
Repair
polymerase (DNA polymerase
I)
DNA Ligase
joins the fragments
(5’ P to 3’ OH)
Initiator proteins
helix opening at replication origin
DNA Polymerase polymerization direction
polymerization (5’-3’)
DNA Primase
synthesis of short RNA primer
Ribonuclease
degradation of RNA primer
Repair polymerase
replace RNA with DNA
Ligase
joining of DNA fragments
DNA Helicase
unzipping DNA helix prior to replication
Single-stranded DNA-binding protein
prevent reanealing
Sliding clamp
keeps DNA polymerase attached to template
and on lagging strand, releases when Okazaki fragment is completed
Telomerase
needed to replicate chromosome ends
Depurination
removal of purines (A and G) from the
sugar
Deamination
removal of NH2 group from cytosine,
converting it to uracil
Thymine dimerization
covalent link between two
adjacent Thymines. Caused
by UV radiation
Somatic cells
can accumulate mutations over
a lifespan that may impact
health
General mechanism
of DNA repair
Excision, Replacement, Ligation
Excision
a nuclease will remove the
damaged/ wrong region
Replacement
DNA polymerase will
synthesize new strand
Ligation
the enzyme ligase will
connect the newly synthesized
nucleotide with the next one (nick
repair)
Transposons
common mobile genetic elements (also called “jumping genes”)
transposase
an enzyme necessary for
transposon mobility
Transposons can make bacteria _______ to antibiotics
resistant
Transposons in eukaryotes
move via an RNA intermediate - retrotransposons
Retroviruses found
only in ______ cells
eukaryotic
RNA is synthesized by ________________
RNA polymerase
Promoter
DNA sequence that is recognized by RNA polymerase as a start point.
Transcription provides _____________ of genetic information
amplification
mRNA
codes for proteins
rRNA
from the core of the ribosomes and catalyze protein synthesis
miRNA
regulate gene expression
tRNA
serve as adapters between mRNA and amino acids during protein synthesis
other small RNAs
used in RNA splicing, telomere maintenance, and many other processes
Sigma factor
subunit of RNA polymerase
3 steps of transcription
1) Initiation
2) Elongation
3) Termination
RNA polymerase
transcribes in only __ direction
one
RNA polymerase in prokaryotes
They have a single type
RNA polymerase in eukaryotes
RNA pol I: most rRNA genes
RNA pol II: protein-encoding genes (makes mRNA)
RNA pol III: tRNA, 5S rRNA, small structural RNA genes
Initiation in prokaryotes
RNA pol can initiate without helper proteins
Initiation in eukaryotes
RNA pols require general transcription factors
Transcript processing in prokaryotes
transcripts are generally NOT processed
Packing of DNA into nucleosomes in eukaryotes because
Prokaryotes do not have nucleosomes
TATA-binding protein (TBP)
is a subunit of TFIID; involved in the
recognition of the promoter
How is RNA Pol II released from the
transcription initiation complex?
Phosphorylation of RNA Pol II by
TFIIH, transcription proceeds
Key steps in Transcription initiation by RNA polymerase II
- General transcription factor TFIID binds to TATA box
TATA box is a conserved sequence found in nearly all
RNA pol II-transcribed promoters and is located ~25
base pairs upstream of transcription start sites - Assembly of transcription initiation complex on promoter
Includes other general factors and RNA Pol II - Disengage RNA pol II from complex to begin transcription
Phosphorylation of RNA pol II tail by TFIIH (kinase) - General transcription factors release from DNA once
transcription begins
Where does transcription take place?
the nucleus
where does translation (protein synthesis) take place?
the cytosol
RNA capping
modification of 5’ end, 7-methylG)
Polyadenylation
modification of 3’ end, polyA tail
Splicing
removal of introns
Exons
expressed sequences
Introns
intervening sequences
What provides a mechanism for functional diversity?
alternative splicing
Translation
conversion of the information in RNA to protein
Deciphering the genetic code
Each trinucleotide is called a ______
Codon
true or false: tRNA is charged when linked to an amino acid
true
aminoacyl-tRNA synthetase
recognizes nucleotides at the anticodon
and the 3’ amino acid-accepting arm to provide specificity
Where is the mRNA mesage decoded?
the ribosome
Ribozyme
RNA molecule with a catalytic activity
There are three bringing sights
A site, P site, E site
A site
(aminoacyl-tRNA) charged tRNA binds to its mRNA codon
P site
(peptidyl-tRNA) condensation of amino acids
E site
(exit): where the “uncharged” tRNA is ejected
What codon codes for methionine?
AUG
DNA polymerase proofreading direction
proofreading (3’-5’)
