Nucleic Acids and Structure Flashcards
____ structure is the sequences of bases along DNA or RNA
primary
___ structure is the formation of a double helix via specific base pairing
secondary
___ structure is the supercoiling of circular DNA or organizing of DNA into chromosomes
tertiary
What are the 3 components needed for DNA sequencing?
primer, DNA polymerase (enzyme), dNTPs, and fluorescent labeled ddNTPs
What enzyme is used in DNA sequencing?
DNA polymerase
What is the role of the primer in DNA synthesis?
starting the process
DNA polymerase extends the primer by adding ______ that ____ _____ with the template strand
nucleotides, base pair
Incorporation of a ddNTP _____ polymerization
terminates
The newly synthesized DNA chains differ by _ _______
1 nucleotide
The terminating bases of all of the newly synthesized DNA strands make-up the _____
unknown sequence
In DNA synthesis, the terminating base pair (ddNTP) is _____ -______
color-coded
ddNTPS differ from DNA in that they lack _____
a 3’ OH group
Instead of a 3’OH ground, ddNTPS have____
H
ddNTPS cannot form a ______ bond with the next incoming nucleotide in a DNA synthesizing reaction because they lack a 3’OH group
3’-5’ phosphodiester bond
The H bond of ddNTPs is ______ reactive
non
B DNA is another term for what type of DNA?
traditional
What are the two types of DNA grooves?
minor and major
The _____ groove of DNA is narrow
minor
The ____ groove of DNA is wide
major
DNA major and minor grooves are formed by _____ _____
backbone strands (of DNA)
What type of bond is a covalent bond that involves a carbohydrate (such as deoxyribose) and is involved in the creation of major and minor grooves
glycosidic bond
The glycosidic bonds not being directly across from each other help cause the ______
major and minor grooves
B-DNA has a width of ____ A
20
B-DNA has a pitch of ____ A
34
B-DNA has _____ base pairs per turn of the double helix
10
B-DNA strands run in what type of direction to each other?
opposite
B-DNA has what type of turn of the helix?
right-handed
What are the 3 types of DNA?
A,B,Z
____ DNA is made when B-DNA is isolated and dried out (looses H2O molecules from the cell)?
A
___ DNA has a similar structure to that of the double helix of RNA and DNA/RNA hybrids
A
____ DNA is formed by synthetic oligonucleotides with an alternating purine-pyrimidine sequence
Z
____ DNA is short and broad, has right-handed turns, and has roughly 11 bp per double helix turn
A
_____ DNA is longer and thinner, has right-handed turns, and has roughly 10 bp per double helix turn
B
_____ DNA is elongated and slim, has left-handed turns, and has roughly 12 bp per double helix turn
Z
A DNA has ____ glocsyl bond conformation
anti (bases are projected away from dexoy. ring)
B DNA has ____ glocysl bond conformation
anti (bases are projected away from dexoy. ring)
Z DNA has _____ glocysl bond comformation
anti at C (bases are projected away from dexoy. ring), syn at G (bases are projected towards dexoy. ring)
______ glycosyl bond conformation has the bases projected away from the deoxy. ring
anti
______ glycosyl bond conformation has the bases projected towards the deoxy. ring
syn
The DNA melting curve plots ___ vs _____
temperature, relative absorbance
What type of light is used on the DNA melting curve?
UV
Tm is ______ of DNA
melting temp
at low temperatures, bases do not absorb as much light because ______
bases are hidden away in the double helix
At high temperatures, bases absorb more light because ______
the base pair bonds (H) are broken and the base pairs are exposed to light
Do all DNA have the same Tm (melting point value)?
no
The more GC bonds, the _____ the melting temp.
higher
The more AT bonds, the ____ the melting temp.
lower
Why do GC bonds melt at higher temps?
GC base pairs need 3 H bonds to pair (so higher energy needed to break) and GC bp have stronger staking interactions
If you heat and then cool DNA too rapidly, _____ base pairing occurs
improper
an improper base pairing be reverse?
yes (called renaturation)
Improper base pairing involves base pairs connecting in a _____ fashion
random
DNA melting and renaturation is ______ reverse
readily
What are the two types of DNA that can form supercoils?
circular and linear
What is supercoiling?
two strands of the double helix being underwound or overwound
Supercoiling puts _____ on the DNA double helix
strain
Compacted DNA via supercoiling _____ the volume of the DNA within the cell
decreases
A DNA loop has a _____ base
fixed
_______ supercoiling is the theoretic method that circles an imaginary circle
toroidal
______ supercoiling is found in prokaryotes
interwound
_____ supercoiling is a combo of toroidal spirals and interwound supercoils and occurs in ______
interwound and toroidal supercoiling, eukaryotes
_____ is the enzyme used in bacteria supercoiling of circular DNA
Topoisomerase 2 (bacterial DNA gyrase)
Another name for bacterial DNA gyrase is ______
topoisomerase 2
Topoisomerase 2 is composed of ______ protein subunits
4 (2A, 2B)
Topoisomerase _____ the DNA strand in 2 spots and then ____ the DNA back together as a supercoil
cuts, links
_____ enzyme cuts one DNA strand
Type 1 topoisomerases
Formation of a _______ structure comes from a palindrome sequence in eukaryotes
cruciform
Formation of a cruciform structure comes from a ______ sequence in eukaryotes
palindrome
A _____ _______ is able to repeat itself when inverted
palindrome sequence
Creation of a cruciform structure from a palindrome sequence allows for the formation of a ____ ____ _____
stem loop structure
What would be the function of the formation of stem loop structures in eukaryotes if they exist?
regulation of gene expression (i.e. binding of RNA polymerase to the correct location)
If it were real, the function of Z DNA would be what?
to regulate gene expression (i.e. binding of RNA polymerase to the correct location
In higher cells (eukaryotes), ___ binds to the DNA negative charge to create “beads on a string” nucleosome filaments
histones
How many histones are in each “bead” on the string?
8
How many times is the helix wrapped around the histone in chromatin fiber?
twice
Beads on a string nucleosome filaments are _____ nm
11
Chromatin fibers are _____ nm
30
Eukaryotic loops are _____ nm
.25
_____ RNA does not have a tertiary structure
M
mRNA does not have a tertiary structure for what reason?
they remain linear without folds in order to not interfere with ribosome bonding and free movement
The _____ structure of tRNA is folded into a _____ structure
cover-leaf, L-shaped
What two types of RNA have tertiary structures?
tRNA, rRNA
The ____ and _____ sides of the tRNA clover-leaf structure ______ _____ on the verticle part and are bent in the middle to create the L-shape
Left, right, fold back
rRNA molecules interact with _____ _____ to form small and large ribosomal subunits
ribosomal proteins
The lower the melting temperature, the higher the _____ bp concentration
AT
The higher the melting temperature, the higher the ______ bp concetration
GC
What enzyme is used to synthesize cDNA strands?
reverse transcriptase
dideoxyonulecotides (ddNTPS) lack a _____ ____ group and a ____ _____ group
3’ OH, 2’ OH
ddNTPS cannot form what type of bond?
3’-5’ phosphodiester
The supercoiling of DNA is facilitated by what enzyme?
DNA gyrase (topoisomerase 2)
