nucleic acids
DNA and RNA are examples; so called because they are found in the nucleus and possess many acidic phosphate groups.
adenine
one of the four aromatic bases found in DNA and RNA; a purine that pairs with thymine (in DNA) and uracil (in RNA).
guanine
one of four aromatic bases found in DNA and RNA; a purine that pairs with cytosine.
cytosine
one of four aromatic bases found in DNA and RNA; a pyrimidine that pairs with guanine.
thymine
one of four aromatic bases found in DNA and RNA; a pyrimidine that pairs with adenine.
genome
all the genetic information in an organism; all of an organisms chromosomes.
chromosome
a single piece of double-stranded DNA; part of the genome of an organism.
DNA gyrase
a prokaryotic enzyme used to twist the single circular chromosome of prokaryotes upon itself to form supercoils.
histones
globular proteins that assist in DNA packaging in eukaryotes. histones form octamers around which DNA is wound to form a nucleosome.
nucleosome
a structure composed of two coils of DNA wrapped around an octet of histone proteins.
nucleoside
a structure composed of a ribose molecule linked to one of the aromatic bases.
chromatin
DNA that is densely packed around histone proteins.
transcription
the enzymatic process of reading a strand of DNA to produce a complementary strand of RNA.
DNA
a long linear polymer found in the nucleus of a cell and formed from nucleotides and shaped like a double helix
RNA
a long linear polymer of nucleotides found in the nucleus but mainly in the cytoplasm of a cell where it is associated with microsomes
translation
the process of reading a strand of mRNA to synthesize protein. protein translation takes place on a ribosome.
mRNA
messenger RNA; the type of RNA that is read by a ribosome to synthesize protein.
ribosome
a structure made of two protein subunits and rRNA; this is the site of protein synthesis in a cell.
rRNA
ribosomal RNA; the type of RNA that associates with ribosomal proteins to make a functional ribosome.
genetic code
the “language of molecular biology that specifies which amino acid corresponds to which three-nucleotide group.
codon
a group of 3 nucleotides that is specific for a particular amino acid, or that specifies “stop translating”.
point mutation
a type of mutation in DNA where a single base is substituted for another.
insertion mutation
a mutation in which one or more extra nucleotides are added into the DNA sequence.
deletion mutation
a mutation in which a nucleotide is removed from the DNA sequence.
frameshift mutation
a mutation caused by the insertion or deletion of base pairs in a gene sequence in DNA such that the reading frame of the gene is altered.
replication
the duplication of DNA
DNA pol
DNA polymerase; an enzyme that replicates DNA. eukaryotes have one version, prokaryotes have three.
primase
an RNA polymerase that creates a primer to initiate DNA replication. DNA pol binds to the primer and elongates it.
helicase
an enzyme that unwinds the double helix of DNA and separates the DNA strands in preparation for DNA replication.
origin of replication
the specific location on an DNA strand where replication begins.
uracil
one of four aromatic bases found in RNA; a pyrimidine that pairs with adenine.
tRNA
transfer RNA; the type of RNA that carries an amino acid from the cytoplasm to the ribosome for incorporation into a growing protein.
hnRNA
heterogenous nuclear RNA; the primary transcript made in eukaryotes before splicing.
splicing
one time of eukaryotic mRNA processing in which introns are removed from the primary transcript and exons are ligated together.
intron
a nucleotide sequence that intervenes between protein-coding sequences.
exons
a nucleotide sequence in RNA that contains protein-coding information; typically separated by introns.
5′ cap
a methylated guanine nucleotide added to the 5′ end of eukaryotic mRNA. necessary to initiate translation of the mRNA.
anticodon
a sequence of three nucleotides that is complementary to a specific codon in mRNA.
70S ribosome
the prokaryotic ribosome
80S ribosome
the eukaryotic ribosome
P site
petidyl-tRNA site; the site on a ribosome where the growing peptide is found during translation.
peptidyl transferase
the enzymatic activity of the ribosome that catalyzes the formation of a peptide bond between amino acids.
Frederick Griffith
used pathogenic and nonpathogenic bacteria to discover transformation
transformation
Process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria
Oswald Avery
tested the ability of inactivated DNA, RNA, and protein to transform live nonpathogenic bacteria
bacteriophages/phages
viruses that infect bacteria
Hershey and Chase
used radioactive sulfur (protein) and phosphorus (DNA) in viruses to trace which could reprogram cells to make more phages
Erwin Chargaff
Chargaff’s Rule: equivalences of A to T and C to G in DNA
Nitrogenous bases of DNA
thymine, adenine, cytosine, guanine
purines
adenine and guanine, 2 rings
pyrimidines
thymine and cytosine, 1 ring
Nitrogenous bases held together by
hydrogen bonds
DNA nucleotide consists of
nitrogenous base, sugar deoxyribose, and phosphate group
double helix
two strands of nucleotides wound about each other; structure of DNA
Rosalind Franklin
produced X-ray diffraction image of DNA
Watson and Crick
built the first model of the double helix
semiconservative model
when a doule helix replicates, each of two daughter molecules will have one old and one new strand
Meselson and Stahl
devised an experiment using a nitrogen isotope to determine the semiconservative model
origins of replication
sites where DNA begins replication
replication fork
y-shaped region where DNA is being unwound
Helicase
enzyme that untwists the double helix at replication fork
single-strand binding proteins
bind to the unpaired DNA strands to stabilize them
primer
RNA chain added to begin DNA replication
primase
enzyme that synthesis primer for DNA replication
DNA polymerases
enzymes that catalyze DNA synthesis by adding new nucleotides, remove RNA primer and replaces it with DNA nucleotides
DNA polymerases can add nucleotides only to the
3′ end of a primer
DNA strand can elongate only in the
5′ to 3′ direction
antiparallel
two strands of DNA are oriented in opposite directions
leading strand
strand of DNA replicating in the continuous 5′-3′ direction towards the replication fork
lagging strand
DNA strand replicating in direction away from the replication fork
DNA replicates in _ direction from the origin or replication
both
Okazaki fragments
segments of the lagging strand synthesized discontinually
DNA ligase
enzyme that joins sugar-phosphate backbones of Okazaki fragments
telomeres
special nucleotide sequences at the end of DNA, do not contain genes, only prevent staggered ends of the daughter molecule from activating the cell’s systems for monitoring DNA damage
telomerase
enzyme that catalyzes lengthening of telomeres
Questions
What two factors are the main determination of the Tm of DNA
Amount of G:C’s & overall strand length
How many rings do purines & pyrimidines have?
Purines: 2
Pyrimidines:1
The DNA from two different species can often be distinguished by a difference in the____.
Ratio of A+T to G+C
What is the difference between Uracil & Thymine
Thymine has a methyl group
What did the X-ray diffraction patterns produced by Rosalind Franklin initially reveal about the DNA molecule?
It is a helical structure with distinct regularities
You have 340 nm of double stranded B form DNA. How many 360 degree turns are present in the double helix?
100
You have 340 nm of double stranded B form DNA. How many nucleotides are present? Be careful!
2000
DNA and RNA both contain phosphate and deoxyribose. (True or False)
False
In general, the keto form of thymine is more abundant than the enol form. (True or False)
True
Left-Handed helical form of DNA
Z-DNA
DNA that results from reduced humidity around the DNA and is more tightly wound
A-DNA
DNA that most closely resembles the Watson & Crick model
B-DNA
Term used to describe the amount of the double helix crossing over itself
Writhe
Number of helical turns in a given space
Twist
What are the main RNA secondary structures?
Bulge-loop, hairpin, pseudoknot, internal loop, and double helix
A closer association between DNA and histones most likely causes___.
repression in gene expression
Which amino acids of histone N-termini can be acetylated and deacetylated?
Lysines
RNA can form Beta Sheets (True or False)
False
What technique is most commonly used to study the secondary structure of RNA?
Computer algorithms
Microarrays involve reassembling configs (true or false)
false
Incubation of cccDNA in 37 degrees Celsius water is highly likely to change the linking number (true or false)
false
DNA wrapped around a histone core
nucleosome
the study of heritable changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence
epigenetics
the combination of histone modifications on a given nucleosome near a gene’s control region affects the efficiency of that gene’s transcription
the histone code
Removes acetyl group from histones
HDAC
methylates histones on lysine 9 of H3
histone methlytransferase
yeast complex involved in chromatin remodeling
SWI/SNF
a mechanism by which cells shut down large sections of chromosomal DNA
gene silencing
acetylates histones in the nucleus
HAT
movement of nucleosomes on DNA
chromatin remodeling
A gene that you are interested in is actively transcribed, causing you to postulate that its promoter is in a nucleosome-free zone. How might you test this?
look to see if the promoter is hypersensitive to DNase
. Histone proteins recognize sequences in the major groove because those sequences have greater rotational freedom. (true or false)
false
Euchromatin is hypoacetylated and thus actively transcribed (true or false)
false
Histone methylation by HMTases can cause a repressive effect, even though the methylation is masking the positive charge similar to acetylation (true or false)
true
One histone modification can influence another (true or false)
true
CRISPR/Cas gene editing approach is specific to a certain target DNA sequence due do what component of the system?
crRNA
A reason for genetic engineering a conditionally expressed allele into an organism is (3 reasons)
1.You can study that gene during specific developmental timepoints
2.It works as an internal control
3.The gene might be essential to development
What protein domain would most likely bind to acetylated lysines in a nucleosome?
Bromodomains
The histone core is an octomer. In addition, there is another histone called H1. Its role is to___.
trigger condensation of the 10 nm fiber into 30 nm fiber
How many nm are there per turn of DNA?
3.4 nm
How far are each basepairs apart in DNA?
.34 nm apart
What is the overall charge of the sugar-phosphate backbone of DNA?
Negative
What forms the major & minor grooves?
Glycosidic bonds
Term used to describe sheer stress protein binding causing an adjacent base to twist
Propeller twist
Type II topoisomerase found in prokaryotes that relieves stress on unwinding DNA during replication by negative supercoiling
Gyrase
Catalytically active RNA strands
Ribozymes
Cohesins
Protein that regulates the separation of sister chromatids during M-phase
Characteristics of Histones (and their tails)
-Comprised of 8 subunits (octamer)
-Tails are enriched with lysine & arginine
-(+) tails mask (-) DNA
-Tails interact with both DNA & other tails
How many types of Histones are there and where are they found?
There are 5; H2A, H2B, H3, & H4 comprise the histone core while H1 is outside the core attached to the linker DNA
What are the 2 types of 30 nm fibers?
- Solenoid (shorter linker DNA)
- Zig-Zag (longer linker DNA)
Ways to change interactions between DNA & Histones
- Nucleosome placement (positioning)
- Nucleosome remodeling
- Histone tail modification
Assay that determines if DNA region is nucleosome-free by using DNAse to cut hypersensitive endonuclease site that will be exposed if region is nucleosome-free. If it is two bands will be shown
Nuclease Sensitivity Assay
- ATP hybridizes to complex
- If conditions are correct complex will form pinchers around core
- Initial conformation is unfavorable & will change
- DNA will move around histone core & a “bulge” of DNA will appear
- Pinchers will release & DNA will move around histone core
Sliding bulge hypothesis
Modifications of histone tails (3)
-Phosphorylation
-Acetylation
-Methylation
Domain that recognizes methyl groups on histones
Chromodomain
Fragments of DNA that contain ori’s of replication within the genome
Autonomous replicating sequences
The complex of proteins that function at the replication fork
replisome
The DNA that is replicated at a specific ori
replicon
Function of Pol I
Replication of new DNA strand and exonuclease activity in both the 5′–>3′ and 3′–>5′ direction
Function of Pol II
Replicates lagging strand while using 3′–>5′ exonuclease activity
Function of Pol III
Replicates leading strand while using 3′–>5′ exonuclease activity
How do Prokaryotes solve the problem of the space left in DNA when the primer is removed?
Primer is removed using 3′–>5′ exonuclease activity of DNA Pol I then Pol I synthesizes DNA in the space
How do Eukaryotes solve the problem of the space left in DNA when the primer is removed?
DNA Pol III will continue to synthesize DNA around primer which will create a RNA “flap” which will eventually be removed by dedicated endonucleases
In what direction is all DNA synthesized?
5′–>3′
How can you measure if the initiator protein is interacting with the replicator sequence on a chromosome
- DNA footprinting
- X-ray crystallography
- Gel electrophoresis mobility shift assay
- CHIP (chromatin immunoprecipitation)
How does Gel electrophoresis mobility shift work?
You run a gel with a lane of just the DNA, just the protein, and a lane with both together. If the protein interacts with the DNA it will move less then the other 2 lanes
How does ChIP work?
You attach a protein to the DNA, shear DNA into smaller fragments, add beads attached to antibodies specific for the targeted protein, purify DNA by removing proteins & beads, sequence DNA to genome to determine what DNA is associated with the protein used
General steps of replication in prokaryotes (circular chromosomes)
- initiator binds to replicator sequence
- Local unwinding
- More initiators bind to same sequence, increasing chance of replication occuring
- Helicase is recruited with loader
- Helicase recruits primase to add primers (helicase also removes initiators)
- Primers signal holoenzyme which recognizes DNA-RNA duplex
- Synthesis of leading strand begins, shortly after lagging strand begins
- Synthesis will continue until two replication forks run into eachother
Floxed
To conditionally delete a gene or segment of a gene using flox technology (uses loxP & Cre-recombinase)
How to use flox technology?
- Insert loxP sites on both sides of desired exon you wish to delete
- Cre-recombinase enzyme will catalyze loxP recombination
- loxP sites will come together forcing the exon into a bulge sticking out of the chromosome
- Exon will be ligated and deleted
What does it mean to control something conditionally & what are 2 examples of conditional controlling?
-To have direct control over expression of gene (such as Cre-recombinase)
-Use a specific promoter sequence (cell specific)
-Use specific response elements from drugs (time specific)
Experimental artifact
Off-target effects from experimental design
Is lysine 9 on H3 repressed or expressed when methylated or acetlyated?
repressed if methylated
expressed if acetylated
Is lysine 5 on H4 repressed or expressed when acetylated?
repressed
Is lysine 12 on H4 repressed or expressed when acetylated?
repressed
Is lysine 8 on H4 repressed or expressed when acetylated?
expressed
Is lysine 16 on H4 expressed or repressed when acetylated?
expressed
Where can methylated cytosines be found?
CpG islands
What type of events have been found to produce methylated cytosines?
Exercisise, starvation, and psychological trauma
Why do telomeres form T-loops? (3)
-DNA damage checkpoints would turn on causing apoptosis
-Unprotected ends can be degraded by DNAse
-Enzymes would recognize it as a strand break & piece two ends together
Telomeres consist of (2 things)
Reverse transcriptase & RNA
What is the advantage of using an IRES in research?
Ability of monitoring a gene of interest without attaching a bulky GDF-reporter
