L8 NUCLEIC ACIDS Flashcards
What is the function of a nucleic acid?
To store and express genetic information.
Nucleic acids are Biopolymers or macromolecules including DNA and RNA
What makes up a nucleioside?
Base + 5-carbon sugar
Define a glycosidic bond.
A covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate
Name the purine nitrogenous bases.
Name the pyrimidine nitrogenous bases.
Name this compound.
Adenosine triphosphate
Name this structure.
Ribose.
Ribose has an -OH group at the 2’ carbon
Name this compound
Deoxyribose
It has only an H on the 2’ carbon
True or false?
Each phosphate compound is added via phosphoannhydride bonds.
True
What type of bond binds the nucleoside base to phosphates?
phosphodiester bond
Name this compound
Adenosine diphosphate (ADP)
Name this compound
Deoxyguanosine
Name this compound
Adenosine
Name this compound
Deoxycytidine
Name this compound
Deoxythymidine
What is the primary structure of DNA?
A sequence of nucleotides
The phosphate of one deoxyribonucleotide binding to the 3’ carbon of another deoxyribonucleotide forms the sugar-phosphate backbone of the DNA (the side of the “ladder”)
What type of bond forms between the complimentary nucleiotide bases of DNA that forms the rungs?
Hydrogen bonds
True or False?
In the primary structure of DNA, the sugar-phosphate backbone is not constant and the bases attach in a selected order.
False.
the sugar-phosphate backbone is constant and the bases are attached randomly
What type of bond forms the stacked rings of DNA?
Van Der Waals
Polynucleotide synthesis illustrates the principle of what in thermodynamics?
Coupling, a thermodynamically favorable reaction (nucleoside triphosphate hydrolysis) driving a thermodynamically unfavorable reaction (polymerization)
True or false?
Hydrolysis of polynucleotides to nucleotides is NOT the thermodynamically favored process.
False
This is why it is coupled to a polymerization reaction
True or false?
The equilibrium of Polynucleotide synthesis lies far to the hydroloysis side (reactant side) of the phosphodiester bond in the aqueous environment of the cell
True
What provides the energy to drive incorporation of the nucleotide into a growing polynucleotide chain?
Cleavage of the anhydride bond in the triphosphate
The polynucleotide has how many residues after polynucleotide synthesis?
n (however many the polynucleotide started with) +1
List the type of state at each number in the picture
- The metastable state = of a weaker bond
- The transitional state
- The stable state = of a stronger bond
Define a Metastable State
A Particular excited state of an atom, nucleus, or other system.
It denotes an intermediate energetic state within a dynamic system other than the system’s state of least energy (the ground state).
________ has a longer lifetime than the ordinary excited states and generally a shorter lifetime than the lowest, often stable, energy state, called the ground state.
Metastable state
How are the structures of Thymine and Uracil different?
The have the same structure except that Uracil doesn’t have the methyl group on the 6’ carbon like thymine does.
Name this compound
Cytosine
Name this compound
Thymine
Name this compound
Guanine
Name this compound
Adenine
Name this compound
Uracil
What is happening in this picture?
Guanine and Cytosine bonding
True or false?
Polynucleotides should undergo hydrolysis under conditions existing in living cells, but this hydrolysis is exceedingly slow in the absence of a catalyst.
True
True or False?
DNA in cells are not sufficiently stable to serve as a repository of genetic information through successive generations
False. DNA cells are suffieciently stable
True or false?
Metastable compounds are thermodynamically favored to break down, do so rapidly, whether a catalyst is used or not.
False.
Metastable compounds are thermodynamically favored to break down, but they do so only slowly unless the reaction is catalyzed
What is the secondary structure of DNA?
The double helix.
3D arrangements of nucleotide residues with respect to one another.
True or False?
The sugar phosphate backbone is ionized and faces outward for favorable interactions with water
True
Nucleic acid bases point _____ and pair up A-T or G-C
Inward
Base pairs are stacked via _______ interactions between heterocyclic rings
Van der waals
How many and what type of bonds are there between adenine and thymine; and guanine and cytosine?
All are hydrogen bonds
Adenine - Thymine = 2 H bonds
Guanine - Cytosine = 3 H bonds
What is the diameter of a duble helix?
2 nanometers which is kept constant
what is the amount of distance between base pairs in a double helix?
0.34 nanometers
A complete (360˚) turn of the helix takes _____; therefore, there are ____ base pairs per turn
3.4 nm; 10 base pairs per turn
_____ is when DNA twists around each other to make a more compact shape which can fit into the nucleus
Supercoiling.
This is the teriary structure of DNA
What causes the the efficient storage of DNA?
Supercoiling
What allows for genetic stability?
The fidelity of DNA replication and delicate DNA repair systems of cells
What is genetic stability?
a low frequency of genetic changes that occur during each round of replication
The _______separates the two strands by breaking H bonds between bases and results in the formation of a _______.
DNA helicase; replication fork
___________bind tightly separated strands of DNA apart in order to prevent the single-stranded regions from reannealing.
Single-stranded DNA-binding proteins
DNA polymerases cannot initiate new DNA synthesis without what?
a preceeding -OH group on the 3’ carbon
DNA synthesis is started by what?
Primase.
It starts the process by making a small piece of RNA called a primer
What is required for DNA polymerase to catalyze chain elongation?
A short ribonucleic acid (RNA) sequence (up to 12 bases long, oligonucleotide), Primer.
The primer also marks the starting point for the construction of the new strand of DNA
When an incoming nucleotide is joined to a primer, it supplies _______, so that the growing strand itself serves as primer for the next polymerization reaction
another free 3′-OH end
__________binds to the primer and will make the new strand of DNA
DNA polymerase
The leading strand, is made _______, adding bases one by one in the 5’ to 3’ direction
Continuously
the lagging strand, cannot be made continuously because of what?
it runs in the opposite direction, 3’ to 5’
DNA polymerase can extend the strand to only how many nucleotides at a time in the direction of 5′ to 3′ from the replication forks?
1000 nucleotides at one time
True or false?
Each Okazaki fragment is NOT started with an RNA primer
False.
DNA polymerase can only make the lagging strand in a series of small chunks called Okazaki fragments because of what?
Because DNA polymerase can only extend the strand in 1000 nucleotides at one time in the 5’ to 3’ direction
________ synthesize new DNA only by adding nucleotides to a 3′-OH group and therefore extend a DNA strand in the 5′ to 3′ direction
DNA polymerases
What are the substrates for DNA polymerases?
The four deoxyribonucleotides:
Deoxyadenosine Triophosphate (dATP)
Deoxyguanine Triophosphate (dGTP)
Deoxycytidine Triophosphate (dCTP)
Deoxythymine Triophosphate (dTTP)
and a single-stranded template DNA
True or False?
DNA polymerase can catalyze the reaction between two free nucleotides.
False.
No DNA polymerase can catalyze the reaction between two free nucleotides, even if one has a 3′-OH group and the other a 5′-phosphate.
Polymerization can occur only if the nucleotide with the 3′-OH group is hydrogen bonded to the template strand.
Once the new DNA has been made, the enzyme _______ removes all the RNA ______ from both strands of DNA.
exonuclease; primers
What happens after exonuclease removes all the RNA primers from both DNA strands?
Another DNA polymerase then fills in the gaps that are left behind with DNA
How is the continuous double strand formed?
the enzyme DNA ligase seals up the fragments of DNA in both strands to form a continuous double strand.
How is DNA replication semiconservative?
DNA replication is semi-conservative because each DNA molecule is made up of one old, conserved strand of DNA and one new one
True or False?
When copying is complete, there will be two double-stranded daughter DNA molecules, each identical in sequence to the parent molecule.
True
True or False?
The unraveling of DNA double helix form the super coil does not cause strain.
False. It does cause strain.
This strain is relieved by enzyme-catalysed cutting and repair of DNA chain
Define Topoisomerases
Topoisomerases are enzymes that modify state of DNA supercoiling
True or False?
For replication and transcription to occur, two parental DNA strands must be separated, and this cannot be accomplished in a supercoiled molecule
True
Which amino acid residues are involved in the chain breaking process?
Tyrosine
How does Topoisomerase II help relieve the strain of DNA unraveling?
Relieves the strain in the DNA helix by temporarily cleaving the DNA chain and crossing an intact strand through the broken strand
How do the Tyrosine residues on Topoisomerase II aid the chain breaking process?
The residues form temporary covalent bonds to DNA that allows the enzyme to break the strand apart to form the gap in which a new strand will be inserted.
What is the mechanism that Topoisomerase II uses?
The enzyme pulls the chains apart to create a gap. The intact strand of DNA is passed through the gap and the break is resealed
True or false?
The rate at which a molecule migrates through a gel matrix in an electric field depends on its dimensions
True
True or False?
The smaller or more compact superhelical forms will move faster than the relaxed forms on in gel electrophoresis.
True
Which of the following statements is not true about DNA secondary structure?
a. There is a minor groove and a major groove.
b. A purine base pairs up with a pyrimidine base.
c. The phosphate groups are positioned to the inside of the structure.
d. The base pairs are stacked.
c. The phosphate groups are positioned to the inside of the structure.
What is the significance of base pairing to the function of DNA?
a. It neutralises basic groups and controls the cell pH.
b. It means that the chains of DNA are complementary allowing replication.
c. It stabilises the molecule such that cell lifetime is increased.
d. It prevents water interacting with the nucleic acid bases.
b. It means that the chains of DNA are complementary allowing replication.
True or False?
The subsequent deamination of methylated cytosine at 5’ position results ina an uracil base which is detected by DNA repair system.
False.
It results in a thymine base.
Uracil only results if deanimated from regular cytosine.
